My Tranny is popping out and is hard to get in to 1st and 2nd, I think I need syncros. Are they easy to service like the Sammies tranny? Or is it something I have to get a shop to do? Are the trannys interchangeable with the 1st gen? http://www.trail-gear.com/samurai-transmission-kits these guys have a kit for $250 but if I open it will I get it back together

Never rebuilt one of these transmissions (manual) but I have experience with a rock crusher 4 spd.  The popping out of gear may be a worn shift fork.  Have you looked at: http://www.drivetrain.com/parts_catalog/manual_transmission_overhaul_kits/suzuki_sidekickand__geo_trackers_overhaul_kit.html

for a rebuild kit?  The manual transmissions in the 2nd generation trucks are referred to as the "M59" tranny for Trackers.  I would only guess the Suzuki GV tranny is very similar if not the same (simply because most parts within my Chevy Trackers have the Suzuki stamp or mold on them).  If you only had stiff shifting issues I would recommend you try a different gear oil in your tranny case like Royal Purple or something, but different fluid probably won't improve a worn fork.  Although I have NOT rebuilt one of these, I would be game to try WITH a good FSM and a really smart guy I could call for questions.   Separating the cases without knicking or chipping them and the small coil springs and detente balls would probably be the biggest pain to navigate through.

Finding one in a junk yard (around here) is next to impossible. Even then it would have high miles and you don't know what you are getting.   GM Parts will sell me a new one for around $2800 so attempting to rebuild one with newer synchronizers is appealing.
http://www.gmpartsdirect.com/catalog/frameset.cfm

I have no idea what a "tranny shop" would charge to rebuild one but I'm of the mind buying a new one would be "more better" than this option because of the labor charges they would have to charge and the fact all the parts would be new: all bearings, seals, forks, shafts, etc.  

My trans had trouble going into gear - I might describe it as stiff shifting.  Turned out to be the clutch release bearing froze up and ruined the spring diaphram part of the clutch assembly.  I had a bad bearing in the trans so I rebuilt that at the same time when I had things out of the car.

Did you have or use any special tools to separate the case halves?

Did you have or use any special tools to separate the case halves?

Not to separate the case.  I did need a gear puller and bearing separator to do the rebuild though. 

the kit that I was going to buy is described as a 99 to 2001 sidekick kit?? when I called them to question them they said there computer showed it as a 91 to 2001 sidekick kit?? but they stopped building them in 98. I am spending a week at my dads house, he is a former mechanic and his friend is a GM mechanic so he should have access to any factory service manuals. the only problem is the kit is 5 to 7 working days away plus shipping time to my dads house so that may put it to my door to late to do it.

EDIT: Just got the full GM service manual for the tranny so I can have page by page instructions