Have you checked for air leaks around the newly installed intake? It's possible that when uninstalling and installing the new intake you could have damaged the turbo inlet, and it's not uncommon for them to tear.
I personally wouldn't be happy with a tune that caused a missfire problem.
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Thanks XJman! I actually completely replaced the box and silicone piping, all the way up to the turbo compressor hard pipe inlet, so should be good there (using this kit, which the tune is designed for: https://www.aemintakes.com/search/product.aspx?prod=21-478wr
I'm 99% sure it's an overpowered FPR that is causing the issue. I've found many people with my exact issue - unfortunately no resolutions though. Since it's essentially a "mechanical issue", and I believe the map is unable to reduce the hot start 100% duty cycle at the beginning, I think there are only a couple of solutions...
1) If possible, change the hot start initial map to a target idle of about 1100-1500RPM. This will allow the ECU to compensate for the extra fuel being added for the first 30 seconds. Then after the pump goes to 33% duty, reduce idle to normal. This is essentially what the cold start map does, though it does it based on the coolant temperature. I haven't spent any time with Subaru maps though (my first ever Subaru, which I only got a few months ago), so I'm not sure what's possible yet.
2) Improve the return flow some how. The FPR is supposed to allow enough fuel back to maintain target pressure. Of course, what's happening now is that the FPR can't evacuate the fuel fast enough, causing an increase in fuel pressure in the rail. Not sure if the FPR design is at fault, or something more fundamental (e.g. return piping restrictions).
Right now it does seem that some people have this issue, and some people don't. I would love to know why there are some people that don't have this issue with a high flow pump. Maybe it's just the ability of the FPR? Maybe the age of the stock FPR? Maybe small differences component tolerances either put you in the problem or no problem camps?
Ideally I'd love to solve this with a small map change. However, if I have to replace the FPR that is fine too. I'd rather not go adjustable if it's a known OEM FPR age issue or something (then I'd just get another OEM FPR).
Appreciate any more insights in to this issue!