Treadstone intercoolers are cheap inefficient cores. Perhaps part of your issue would be heat soak and cooling efficiency. On my treadstone intercoolers I had issues keeping charge temps cool anything above 23-24 psi on T04E 60 trim running pump. Some days it would be good others it would be not. When I switched to a pte (garret core intercooler) it changed everything. We were able to run 30 psi on pump and IATs were alot more stable (post intercooler). Also I haven't seen flow bench numbers but perhaps the intake does run lean in cylinders 2/3 much like the factory intake does. What sort of AFRs were you seeing overall? Perhaps run a richer tune? The evo guys generally run low 11, high 10 afrs for this exact reason unless they are running race gas. No disrespect but if I had built your engine I wouldn't warranty for the damage either. The rear main seal you have a legitimate gripe I will admit.
Can you quantify what you think is heat soak and cooling inefficiency? BAT was never a problem with the tr8 previously, let alone with the tr1035 I was running at the time. IAT was in check as well. The ST manifold has pretty damn good even airflow to all 4 cylinders. Much better than the imbalance of the oem manifold. It may not flow the most, but it's documented to be one of the most even flowing. AFR appeared to be in check and at a safe level through the tune and datalogs. However, cylinders 1 and 4 were running richer than 2 and 3 to compensate and reach target AFR
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