Im new to the site so I dont know if this has been posted before. I have a 2nd generation 350 which I have completely machined and rebuilt inside out. I plan to put this into a jeep I building just playing around I want a manual transmission but have no clue what to go with or if I can use a jeep tranny with adapter. My guess is the motor will have around 300hp. any comments will help  

I would suggest that if you decided on manual route that you either use a HD NV4500 or MD NV3500. Either one would work though 4500 is stronger and has a deeper granny gear. I would not waste time with old 4 speed as 5 speeds area lot more flexible and shift better too. If you go 4500 route, stay away for Dodge 4500's earlier than about 99 and GM used to different bell housings for 4500 from 92 to 94 and 95 till 2000 on SB 350 when the SB dropped from P/U trucks. All GM 4500's are 32 spline and dodge can be 23 or 27. GM 3500 should be 32 spline too. The really nice thing about OD trannies (auto or manual) is that it lets you run much deeper axle ratio and still have a nice cruise RPM. Example when you use a early GM 4500, it has a 6.34 first gear and a .75 OD. When you gear axle for same overall ratio/cruise in top gear with a 4500 vs a SM465 while the 465 has a 6.56 first gear "crawl" ratio, when you couple the 4500 to deeper axle gears (because OD lets gives you a wider ratio range on final drive ratio) your net result is 6.34 / .75 or 8.45 to 1 from highest to lowest gear. Even a 3500 with a 4.02 first gear will "feel" like a 5.50 to 1 first gear because of wider ratio range that OD adds.  

what yearsare good for the nv3500  

You want a 93 and later one from a GM truck. They made a few tranny designs before 93 that look like 3500 and are sometimes called 3500 but they are not though they will swap/bolt in place of one another. In 93 the true NV3500 was born and has not really changed since as it has proven reliable. (even Jeep started using them in 2001 as a 3500 in a special case design so that it was a bolt in swap for the AX15 it replaced. (this 3500 bolt in is a officially called a NV3550) do stay away from Dodge NV3500 as they have a taller first and second gear than GM 3500's. (Jeep 3550 has same ratios as GM version but different case) Also be advised that these trannies DO NOT use gear oil, they use GM syncromesh fluid. (Dodge makes a compatible fluid too)