After recently RE-putting my bike back together, (timing issues) and firing her up, the right cylinder would not fire. had everything, spark, fuel, air.

Eventually it did re-fire, but now there is a loud, irregular tap/knock only when both plugs are in. As in, when running on just the left cylinder, as before, it ran farely well and revved fairly freely, but when but both cylinders are plugged in, clunk clunk.

Not valve shims, i checked those, (the beginning of this whole fiasco)
Not regular cam noise ( both cams already have side shims, and it wouldnt cause the puttering near death)

Unless i bent something (don't think so, that was previously the good cylinder before i started tearing the ol girl apart) I'm thinking maybe my cam chain tensioner isn't tight enough? would that cause some slippage and clunkage?

3rdish post, 3rdish question, thanks guys, trying to revive Sooky the Suzuki,

it could be a connecting rod bearing thats what i just had to deal with.

scary stuff

Sure sounds like a duff bearing. An oil pressure test will highlight a suspect bearing but you will need to beg/borrow/steal the equipment needed to carry it out. Under the pickup cover on the RH side you will see a large silver bolt, removing this gives access to the main oil gallery. The pressure gauge screws in here, you are looking for a figure of between 30 and 70 psi at 3krpm with an oil temp of about 60c.
Maybe get a pro to do it, and a compression test at the same time wouldnt be a bad idea.

Would a messed up bearing make a clunk when the cylinder isn't firing, but still moving? When the plug boot isn't connected, no clunk. But everything is still spinning.

It's as if the little explosions are making the racket. Whats that all about?

From reading your original question, it sounds like you took the top end apart and left the bottom intact... correct?  and the right cylinder wasn't knocking before you started this operation, correct?  If so, I'm thinking you didn't degree the camshaft on the right cylinder correctly, so now you have a timing issue in the right cylinder that's causing the knocking.  Cam chain affects both cylinders, so I'd say that's not a suspect.