Only runs 40 Degrees advanced
5* of what? Crank or cam timing?
Crank timing. His 40 was really 35.
I can tell you I've seen many "pro" engine assemblers who can't find and verify (and correct) TDC or degree a cam. They almost never check P/V clearance and if they do, they do it wrong and give up compression and leave way too much clearance.
That's why it's so expensive to assemble an engine. I've done some engines on their first build that need to be mock assembled 8-10 times to check and verify and correct things. Everything SHOULD be written down, on paper so there is a record of it, and when the engine comes back it, the sheet pulled and all the numbers verified on disassembly.
Time is money and it costs to do it right. I feel bad because the OP spent a ton of time getting this sorted and it should have been done on assemble. So in the long run, the time and frustration was way more than the cost of doing it correctly.
Again, I'm glad the OP got it sorted out and found the issue. But it's a bummer how much time and energy he spent getting it done.