ok so high flow cat is ok. now I'm thinking of running a 2.5" system could I get a 3" cat or would that cause a crazy turbulence in the system and stay with the 2.5" set up. Also with me changing my front header and cross over will the bolt into the stock rear header?

At your mod level, it won't necessarily hurt, only position you for future mods.

Plog and cross over should boltup if you stick with a stocker and coat it. shouldn't hurt anything. Although you should skew your front injectors by 2% IIRC.

that where you can come in my friend can you help my tune my car once this all gets done

Another thing now. ( I should write all my ideas down) I see the down pipe for the bonneville is either off road or they weld on the cat. Will a 3" down pipe hook up to my stock rear header? or will I have to get the 2.5" off road and cut out where the cat goes, OR, will ZZP make a 2.5 down pipe with a 3" cat for me you think? I dont want to loose too much back pressure and torque I really want to use a 2.5 downpipe or will a 3" be the best. I am N/A btw