What is the clunking and poping even in neutral?

What is your question?

My 1999 yukon Denali pops and clunks when its cold and also shutters like its going to shut off, but it stops after I gun it and it warms up plus there is a smell like burning or somthing. I have greased slip yoke, removed fuses(T-Case, 4wd and cruse control fuse) trying to trace the problem. Starting to get really tried of this thing, think i may just run over it with my lifted Ford F-350. My sister had the transmission replaced about a year ago while she owned it, and thats why i cant figure out what the deal is. It throws the check engine light on, but after it smooths out the engine light goes off. Think i covered it all, please any help would be greatly appreciated. Thanks