Diesel Bombers - 98.5 cummins Tranny problems

ok well i cant figure this out ive had the truck for 5 months and its been like this (yes i know that is bad) ok this is a rundown of the truck, its a 98.5 24v qclb 4x4 auto with 187000 its fire ringed 150hp injectors, cai, big gulp, 7blade turbo 5inch straight piped edge juice with attitude, fass fuel pump with 1/2 inch line the stock pump was completely removed and a stock tranny hahaha hmm that might be the start of the problem i bought the truck this way for 5 grand no rust came from new mexico, so the problem.... the only way it shifts from 1-2 is i have to put it into neutral then back into drive and the same goes for 2-3 after im in 3rd it shifts fine ive been putting it off and driving it like that because personal problems but i can now start to mess with it so any help with what it might be would be appreciated