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Head gaskets, EGR cooler, oil cooler, all injectors, coolant bottle, EVERYTHING was replaced. $8900 without the ARP's. I supplied those. It still pushes coolant out the bottle until it overheats.
Did they machine or replace the heads when they were installing the ARPs? I noticed that you just said head gaskets were replaced didn't mention the heads were or not. If they didn't do that, then even with the ARPs you'll still have problems with leaking coolant. I doubt the blocked off the EGR either, so that will be another trouble spot that will have to be overcome if your going to add tuner and stuff like that to it. There are driving considerations you can do with a stock truck that would mitigate problems with the EGR and EGR cooler that you can do, but not if it's going to be tuned.
Stick with 4" exhaust turbo back unless your planning on doing injectors and turbo upgrades. If your just at most going to do a tuner, 4" will do fine by you. If you actually go higher then 4" and your not pushing enough flow thru the exhaust(like you would with bigger turbo and injectors) you'll be sacrificing some low end performance.
Like dcaddi2 said, it's mainly for lower egt's and sound(especially if you straight pipe it). MBRP tends to be the favorite with the 6.0s owners. I have heard some good things about silverline and the others, just going by numbers though tend to favor MBRP.