Sounds to my like you've tried all the "usual suspects".

I was going to suggest the Active State PDK (Perl Dev Kit), but I went to the AS website and evidently they no longer sell licenses as a standalone product. That vastly increases the cost. I bought a license 15+ years ago, sure hope that I can continue to get updates because this thing works amazingly well with many features that the open source packaging tools don't have.

I think you are probably aware of this, but for others, here is the official link to the PE spec: MS PE/COFF specification. Yes, it is complex. I suspect that some sort of checksum or what MS calls the Authenticode PE Image Hash is not being updated correctly. That sounds it would cause the "exe actually works, but throws a bunch of error msgs" problem.

There is a report from stevieb that VS 2013 has some sort of issue with modifying the .exe header information. That surprised me. Whether or not VS would work in your situation probably has to do with the compiler,linker,etc that you are using to generate the .exe.

I don't know how interested you are (meaning how much work you want to put into this), but since the specs are public information, an effort to update the appropriate Perl module would in theory succeed. I would be willing to assist.