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Theoretically, you could remove camshafts in any position if you are careful enough to loosen camshaft bolts in cross pattern 1/4 of the turn each time. Removal of camshaft in some specific position was suggested in order to have the least pressure on them while working.
Putting them back in the correct position, while having crankshaft "on the mark" (TDC of piston #1), should make sure your valves timing is fine.
Camshaft jumped because it had pressure applied on it by valve lifters. If camshaft cover is still not broken, everything is fine.
You should check position of crankshaft and if it's not "on the mark" any more, you should rotate it until it reaches the mark. While doing so, make sure cam chain is fastened high enough while still being able to move (or just ask somebody to hold it by the hand and release slowly).
You don't have to move crankshaft - you only need to align correctly camshafts.
Crankshaft position defines position of pistons in cylinder. Cycle (compression or exhaust) is defined by position of camshafts.
So, to change cycle you just need to mount camshafts 180 degrees different to positions they were in at the moment you removed them. I have explained how to achieve that in my previous post. There will be no timing issues if you manage to keep marks on both sprockets as defined.
I have managed to reduce a bit clicking sound by tightening up chain tensioner as described in manual (tightening up by hand until it reaches the chain - you'll feel the difference in force needed, and than making an additional 1/4 of the turn using some tool).
Rest of the clicking I would connect to valve clearances which I have set to upper limit, so I can imagine camshaft lobes are hitting valve lifters "from a bit bigger height" or "under a bit steeper angle".
BTW, bike starts really easy and clicking is audible only on idle.
I currently do not ride my bike yet (it's still in winter sleep), so I still have to go to some professional mechanic to ask if that clicking is "inside normal boundaries" and confirm engine power and fuel consumption is fine.
First, for me your camshafts look fine. Couple of abrasions on sliding part are not longitudinal, so I cannot imagine they were made because of movement/friction. A bit of rust on camshaft lobes should not be an issue, as they are on the part which should (theoretically) not touch valve lifter nor anything else. Maybe you could try removing them by some fine grain sandpaper.
Than again, I'm just a rookie as you are, so it' better if somebody more experienced comments on this.
I gave up of removal of camshaft sprocket, as I did not have correct tools. Either way, on second thought, I guess that diagram in service manual shows valve lifting lobe and not protrusion next to sprocket hole. It's just not clearly marked.
Regarding putting back the camshafts:
One turn of the crankshaft (360 degrees) equals 1/2 turn of the camshafts (180 degrees). So, you can have line mark on the generator visible in 2 different positions of camshafts. One position is top dead center (TDC) of compression cycle, while next position (360 crankshaft degrees away) is TDC of exhaust cycle.
Both you and I have removed camshafts in "wrong position" - TDC of compression cycle of piston #1, which is meant for valve clearance measurement, while TDC of exhaust cycle should be used for camshafts removal (there's less pressure on camshafts in that position).
I would not recommend trying put them back in the same position. Instead, you should put them in the "correct position", when "I" sign on intake camshaft points to the rear of the bike. You can do it without any crankshaft rotation, as by putting back camshafts in some specific position you are defining which cycle engine is in. Just make sure mark on generator is visible - crankshaft was not moved in the meanwhile:
Before putting camshaft caps/holders, position intake camshaft as described in the manual (red arrow):
Exhaust camshaft has symmetrical marks, but you should make sure lobes of cylinder #1 (further away from sprocket) are positioned as in manual:
Next thing is to put cam chain on EXHAUST sprocket as tight as possible WITHOUT rotating crankshaft. Once you did it, install and carefully tighten exhaust camshaft cap, taking care about lubrication tips and cross tightening instructions from manual.
Next, you have to put chain on the INTAKE sprocket as tight as possible, while keeping sprocket mark "I" correctly aligned. You can rotate intake sprocket a bit clockwise to catch correct tooth with the chain, and then rotate it back with chain on it in order to achieve mark "I" alignment. Chain portion between two sprocket should be really tight.
(Video made before I removed camshafts)
Now, before you put INTAKE sprocket cap and start tightening it, I would recommend fixing chain on the intake sprocket by zip tie firmly (blue arrow in my intake sprocket photo), as from my experience chain tend to jump/skip one tooth while tightening the cap. This is caused by tension on the chain being present only from the right-hand side, while left-hand side is loose until chain tensioner is installed. So, remove zip tie only once you have installed and released cam chain tensioner.
Let's hear what other have to say.
magiccube Let me know if you have any additional questions.
I would install the cooler...
I did that, thx!
After assembling, I got famous Yama-tick sound.
I don't know if it was there before or it's just louder now as plastic covers are removed and I'm in a concrete garage.
It can also be from a bit bigger valve clearance, as I increase it close or to max value (all of them were close to minimum or below, so trend is going down).
One practical question:
Once you have achieved desired valve clearances and mounted that bloody cylinder head cover, do you try starting the engine without cooler to check if it is running, or that could hurt cooling pump (to run without a fluid for some seconds)?
I mean, it would be much better to realize that I have to open and rework everything again before I mount cooler and pour fresh cooling fluid in the system...
OK, to answer my own question:
Yes, somebody has put sprocket 180 degrees wrong - lobe on the camshaft is nest to "I" instead of "E"
That strange, as I own my bike from 8k km and now it has 41k km. Nobody should mess around with camshafts before me.
Anyway, I'll consider should I rotate the sprocket or just mount camshaft back the same way it was before opening.
I got pretty regular results.
Intake:
0.12 mm
0.14 mm
0.13 mm
0.12 mmExhaust:
0.23 mm
0.25 mm
0.24 mm
0.23 mmNevertheless, in TDP of cylinder #1 (Left Hand Side)
during the compression cycle (crankshaft lobes point outside)
PXL_20240224_133113501.jpgPXL_20240224_133156805.jpg
I got "I" mark on income crankshaft sprocket aligned with cylinder head edge, but on the front instead of back side.
Is it possible that that particular crankshaft sprocket was mounted 180 degrees opposite to needed orientation?
Thx a lot guys!
Now, as you were so good, I have a next question:
While buying all needed spare parts in local Yamaha dealership, clerk told me I should also replace 5 rubber dampers through which cover bolts are screwed - 5VY-1111G-00. They are pretty expensive (13.5€ each) and service manual does not mark them as parts to be replaced every time, just lubricated with silicon grease.
What is your approach?
Do you change those dampers or just inspect them?
Another question:
What do you use as a lubricant on areas marked to be lubricated by Molybdenum disulfide oil ?
Yamaha dealer asks almost 30€ for it and it's more expensive than a rubber gasket I have to get.
That's why I was wondering if some 3rd party product would be good enough, like this one:
Guys, official service manual mentions use of some special bond when mounting new gasket:
Is it necessary to use this bond and which other product I could use if I cannot acquire the original Yamaha bond?
Indeed seat does not fit:
A super-kind staff from http://www.wkmoto-shop.de has put the seat on an old Tracer to test it, and it turns out seat hits tank in front of it and cannot be mounted correctly.
20231115_111737.jpg20231115_111626.jpg
Lowering the original seat would be shaving off some foam below the cover?
How much can be achieved that way, while still not sitting on the plastic? 10 - 20mm ?
This is a very bad news. 
I am looking for Yamaha Tracer 700 2016 lower seat and there is no OEM part.
On the other hand, Tracer 700 2020 lowered seat is:
B4T-F47C0-00
https://www.yamaha-satzteil.de/product_info.php?products_id=525117
Did anyone ever tried to put any Tracer 700 2020 or Tracer 7 seat on older Tracer 700 2016-2019?
Now it's better: Vernier caliper set to 30mm misses ~2mm to reach lower part of chain guard
After ~1500km new chain become a bit loose, so I had to tighten it up again.
As I am never sure I'm doing this right, I would like to ask for your opinion.
Manual says 30 - 35mm from chain guard to middle of the chain:
Screenshot_20230915-165906~2.jpg
My chain seems to fit into this range:
and still can reach chain guard easily:
Still, I'm worried I've tightened it too much.
Should slack be measured from the wide (yellow) or narrow (red) part of chain guard?
So, it seems new sprocket fixed the issue, although it looks very similar to the old one (except for the rubber dumper):
I would like to use this opportunity to thank all the specialists for saving me! 
If I go for changing the sprockets, do I really need to change front sprocket nut too, or I can re-use the existing one?
We have specialists here for combining new chains with old gear sets, I think they will know what to do
But seriously, have you really checked the correct alignment of the rear wheel? I know this RtrtrtRtrtrtRTrtrt... effect from misaligned chain drives while pushing the bike backwards.
That doesn't look good, I wouldn't drive like that with more than 50 km/h.
I just came back from aligning rear wheel with laser. I have put all my hope in that... But nothing changed. Not even the intensity of the sound.
I can only imagine that front sprocket is "too wide" between teeth, so that chain ends up being pulled by just one of them.
That one tooth catches the chain and keeps it "locked" for too long (too far).
Or, that's at least how I imagine it. 
Please, 'specialists for combining new chains with old sprockets' help me!
OK, I have put new DID 525 ZVM-X2 114 links chain and... I makes horrible noises.
If I use engine brake or just engage clutch, chain is silent.
Nevertheless, as soon as chain is pulling bike forward, even at speed of 2km/h, it makes very strange noise:
First I thought it's about the plastic cover of the front sprocket, so I removed it and repeated the test.
Nothing changed.
It seems (also a bit visible in the second video) that chain does not leave front sprocket easily. It seems it's lifted after it and hits rubber glider on the rear swingarm (from below).
Tightening up the chain did not make any difference.
Any idea what can it be and why chain does not leave front sprocket as it should?