2003 GMC Sierra problems!

[Mudslut07]

My biddy has a 2003 GMC Sierra SLE 4x4 5.3l. The truck stared as stock but he decided to jack it up and start messing with mods,long story short,a nice truck went to a mud beater real fast and things went downhill from there. The tranny he has in it now was rebuilt maybe 6,000 miles ago and had a shift kit put in. He also installed a tb spacer and a superchips programmer. The truck ran awesome for awhile but then the service brake system light started going crazy and he lost 3rd and overdrive. He went to a local junkyard and got a whole new wiring harness from the cpu to the trans/transfer case and put it on,he claimed this fixed it for a few days. Now he is thinking it's his tps sensor? Anyone have any input at all?

Thanks in advance