I have a set of works shocks from a trx90 honda. They appear to be the same mounting as the LT80 yet are a little bit longer. Will I run into any problems by putting them on the LT80?

The only thing I could figure would be the camber of the wheels.

 

Should be ok. Call ATVracing1.com and ask them. I would suggest buying his LT80 A-arms.

 

I have been looking at his A-Arms nice stuff!

I just purchased an Fmf Fatty Pipe with silencer today from a local dealer closing his doors. It is a used pipe and muffler. I don't have much experience with these. Do I need to rejet the bike after this is installed?

 

Yeah depending on how much too long the shocks are they will make the top of the tire lean outwards and it will make the quad a little tippier in the corners.I tried some longer shocks on our Viper a few years ago and swapped back to the originals as the extra travel wasn't worth it...Longer A-arms or even some wheel spacers will put some extra leverage on the shocks and probably bring them back in line if they are close to being the right length.

 

Send them back to works and have them made for the LT. Like yeller said, the camber caused by the added length is not good.
As far as the FMF, just watch the plug color.