Disclaimer
Every effort has been made to ensure that this guide is as accurate as possible, by following this guide you will doing so at your own risk. If you feel that you do not have the capabilities for the job then please seek the help of a professional mechanic. In no event will this forum or myself be held liable for any damage including without limitation, indirect or consequential damage that may possibly occur.
The problem with not removing the cam covers (well one cover anyway) is you may be at TDC but not on the compression stroke, in which case the cam chain will jump over the cam sprockets and you will then have a lot bigger job on, than just changing the CCT's, as you will have to re-set the valve timing!
The following imo is the quickest and safest way I've found to replace the CCT's
(1) Remove seat.
(2) Disconnect block connector on end of wiring from fuel tank (located under-seat in front of battery box).
(3) Unbolt fuel tank, turn fuel tap off with 8mm open end spanner and disconnect all hoses noting where each one goes first (use masking tape and write on it if you won't remember) then lift off tank (easier to do when tank is nearly empty).
(4) Remove air filter box lid and air filter, then remove the two air intake trumpets, (noting where each one goes as they are different lengths) cover the intake holes of each carb with a clean rag so nothing can fall in there, next remove the screws holding the air box to the carbs and disconnect the breather hoses then remove the air box itself.
(5) Remove the spark plugs and cover holes with clean rags
(6) Remove the two caps from the alternator housing (left-hand side of bike when sitting on it) be very careful removing the center one as it's made of very soft material.
(7) Using a socket and tee bar in the center hole of the alternator cover turn the engine over (anti-clockwise) until the timing mark 'RT' lines up with the mark on the alternator cover which can be seen in the 2nd hole of the alternator cover.
(8 ) Remove the rear cam cover (it's much easier than the front one) also note models with the pair system will have a metal locating dowel between cylinder head and cam cover, not applicable on UK models.
(9) Now looking at the camshafts, the lobes should be facing to-wards each other, if not turn the engine over one full turn (360 degrees) until the 'RT' mark is re-aligned, they should now be facing to-wards each other and the marks RI and RE on the camshaft sprockets should be level with the top part of the cylinder head and will be facing away from each other, you are now ready to remove the rear CCT.
(10) Unscrew the small bolt in the end of the rear CCT and remove it along with the alloy sealing washer. Next turn the screw head inside the CCT clockwise two full turns, lock it off in position using a locking key. The Haynes Workshop Manual shows you how to make a simple locking key. Tape the key in place once you've locked the tensioner off, as you don't want the key jumping out. Next undo and remove the CCT.
(11) Clean off mating surfaces, fit new gasket and new CCT, (they come already retracted) once fully tightened up you can release the CCT plunger making sure it unwinds slowly until full tension is released, then remove tensioning tool and re-fit sealing washer and bolt, then re-fit cam cover. REMEMBER TO TAKE THE METAL CAPS OFF THE OLD CCT PLUNGER HEADS AND FIT ONTO THE NEW ONES, AS THE NEW ONES ARE NOT SUPPLIED WITH THEM!!!!!!.
(12) Now turn the engine over anti-clockwise 450 degrees (one and a quarter turns) until the 'FT' mark lines up with the mark on the alternator cover, you are now ready to remove the front CCT using the same procedure as the rear, without the need to remove the front cam cover.
(13) Re-fit everything else in the reverse order of removal, I used a little thread lock on the screws that hold the base of the air box to the carbs.
Once you have finished re-fitting the CCT's, before putting it all back together turn over the engine 3 or 4 complete turns using the socket and tee bar (anti-clockwise) just to make sure everything is turning freely before you start the engine!
I hope that info is helpful to you!
TIPS:-
(A) I think it best if you try to see if you can undo the center cap in the alternator cover first before starting to strip the rest (remembering what I said about them being of a soft metal).
(B) Make sure you only turn the engine over by hand ANTI-CLOCKWISE otherwise you will be putting extra load onto the CCT's which you really want to avoid.
(C) Also don't forget to turn the fuel tap back on when re-fitting the tank! The later 19ltr fuel tank models don't have a manual fuel tap.
Cheers,
Chris.
Probably a little late now, but here goes anyway.
Or did you mean because the cam chain is slightly stretched the marks don't line up exactly 
