3 questions ... thud ... hesitation ... tick

Hi, I have three problems all separate, so if anyone has any insight please feel free to comment.

The first...

This hasn't happened that often .. maybe 5 or 6 times .. if I am trying to accelerate quickly and shift from first too say second ... but say I shift a little too low in the rpm's I have heard a thud sound ... not sure if it is coming from the transmission, or the rear end or elsewhere. But it was a rather loud thud and I have no idea what it could be.

Second..

Sometimes when accelerating ... say in second gear ... low rpm's and I give it some gas to try to really get going .. it seems like it hesitates ... not instantly .. like the car starts to accelerate faster but it takes sometimes 3 or 4 seconds then it kinda just all of a sudden kicks in. Could this have to do with timing? Or could there be other reasons??

About the same old tick ... I finally got my pacesetter o/r x pipe and it is sitting in the garage.. but I have to take it with the original exhaust to get an emissions test. 15 days ago... anyways so I am getting a temp pass and have to drive the rest of the gas out of it.. bought that guarantee to pass stuff.. so I need to run it out of the system... anyways there is an extremely audible ticking which I am sure is an exhaust leak from the flange from the original h to the headers which I am hoping they don't catch for the emissions.. I don't want to repair it before only to rip it down after to put the x pipe on. So we'll hope for the best.. my dad doesn't seem to believe that the exhaust leak would be making this noise and I desperately want to be right... kinda justified buying my new headers and x pipe. lol

Ya hopefully its just that...about the thud... and I have brand new plugs, cap and rotor, new wires, I also bought new vacuum lines, just put a cold air intake on so the air cleaner is good, just did a oil change. Only real tune up type of thing I haven't done is change the fuel filter... could this cause hesitation?

Another quick question if you guys don't mind.. about grinding gears.. going from 2nd to third.. syncro's gone? Would or could a short throw with adjustable stops help?

Hey Jricher, I'm not getting any error codes... cleared them all up a few months back, could bad timing cause hesitation and would bad timing put out error codes? And about the exhaust I hope I'm right, but I heard that thump again today, almost right below me, transmission I think, but I wasn't pushing it that hard at all.. just low rpm's in second gear??