So long story short, bought a beat to crap 2004 Crewcab F350 4x4 for $5000, bulletproofed the engine and repainted the whole truck runs awesome

... except for the trans. Guy I bought it from had an Edge Juice on it.... So this is what I'm experiencing:
-Bad shake at low speeds/take off. Only happens once and a while. Replaced carrier bearing on axle thinking it could be that. And I replaced both trans filters and changed the fluid, seemed to get a little better, but is still there every once and a while. Might be the torque converter?
-Feels like its slipping or hitting neutral when it shifts gears, only sometimes on the lower gears. Above 45-50mph shifts good, shifts are firm. With the stock tune its really bad, with my Looney tune on it its not as bad.
Any input from you guys with I might be looking at, before I get the motivation to pull the trans out?
Thanks for the help. Wouldn't be able to get this far along on the truck if it wasn't for you guy!!