Not saying it isn't, but that might not be the issue.
Sounds like fuel starvation, low pressure.

Check fuel pressure first. The FPCM default/normal setting is typically 43psi; when it sees an issue, 55+psi.
So, regardless, the fuel should be flowing, the FPCM won't do that, unless there is a wiring issue or install error.
All the installs we've done, FPCM doesn't care what pump is being controlled, as long as it's "acting" like a stock one.