That doesn't make sense. You set the valve clearance when on the base circle so there is no pressure againts the valve your checking. Chain slack does not matter in any way what so ever as the cam is not touching the valve during inspection. Sure it can affect valve timing, but thats not what your checking when doing clearances. As for the coil packs, after the 3rd or 4th spark plug swap I stopped getting good clicks as well, even when applying mechanical leverage. I've got enough miles on the bike to be pretty sure they have been seated correctly.

 

My coil packs don't really snap in either, well only one does. If i tried to push them in any harder the engine would fall off! It seems to run fine and the mechanic didn't see anything wrong either when I took it in.

About having the cct off: Having done valves a couple times I don't think it matters for checking clearance as long as you aren't cranking with the chain guard/camshaft holder off. I did that once and it skipped while i hand cranked, had to re set the timing. -facepalm-

 

I was pressing really really hard to get those spark plug caps on but got only got a slight click on one or two cylinders.
I didn't notice any change when I loosened the cam chain tensioner. It only made a difference when I had to remove the cam to reshim it.
This bike has a manual cam chain tensioner from one of the previous owners. Upon reassembly I just put it back at the tension it was at before. It seems fine, doesn't make any weird noises or anything, but I'm starting to wonder if I should have gone and found information on how to set the tension properly because the previous owner may or may not have set it too tight. Of course there was nothing in the service manual about this because the bike comes with an automatic tensioner.
Also the big bolt on the mcct appears to be leaking oil and I don't know how I would seal the threds. It wasn't much though so I just put it back together without much concern for it.

"so the back side of the chain is tight, that way your cam to crank timing is right on the money. if the tensioner is removed or loose (and who knows what kind of condition it's in), timing can vary by the amount of slack on the front of the chain"

As long as I'm rotating the engine clockwise only, any slack in the back side should be irrelevant since there will always be tension on the front side pulling the cams. It would only matter if the crank started to twist back counterclockwise in which case the slack would shift to the front and the cams would be ever so slightly out of time with the crank. Even that wouldn't affect valve clearances since the cams would still be where we want them, and everything would line back up again when the crank starts to turn forward again.