Just delete it i would if it was mine. I would hate to do all that work and the cooler crap out a month down the road or 5 years down the road delete it and be done with it.
Check to make sure all converter nuts/bolts are tight. Did you have noise when you first drove truck after rebuild did you get down on it after build could be Flexplate. I would double check converter though.
Easy place to look first is EGR Valve/Cooler losing any coolant. Not externally cooler could be cracked and leaking coolant to exhaust first pull egr valve and check for moisture in where valve goes in.
I have our level two transmission in my Excursion now for 3 years it has 200cc injectors precision turbo stealth stage 1 hpop regulated return i drive it daily have ran it at drag strip and hooked to the sled no problems at all we stand behind our work. You will not be upset by going with our...