Wow... that looks ridiculously clean!! Upping the power is pretty much all revolving around the turbo... helping it breath easier = exhaust work, intake work, intercooler... increasing and controlling boost = boost controller... then the next steps is generally injectors, ecu and bigger turbo etc. B...
I was only aware of the exhaust causing overboost issues in JZA80 and JZS147/161. Never heard of it on a TT 1JZ. Do you have stock turbo y-pipe? If so that should be creating well enough restriction to stop creep. I would be looking for other causes... split hose to wastegate, washers under wastegat...