Answered the questions. Will the updated top hat make a difference? What version you running?
The updated hat shouldn't make a difference at all EXCEPT if you have the version which was made before the 400/465lph pumps came out. If you have one of the hats that was made before then the basket is too tall and will bottom out the pumps. To verify which hat you have you can measure the basket that the pumps sit in. The version that's compatible with the 400/465 pumps should measure .97" tall. If your basket is taller than that your pumps will without a doubt be pressed against the floor of the tank and starve them of fuel.
Regarding the other questions I asked I have a few more..
Wiring- What color wire at the FPDM did you use to trigger the relays?
Tune- Has your tuner properly set your tune up for a return style fuel system?
Yes, but this is still in progress, but the pumps drop 20 psi at wot .
I'm not sure what still in progress means. Either the calibration has been converted or not. I would speak to your tuner about this and find out for sure if indeed it's been converted or not.
If your tuner hasn't completely finished setting your car up for a return style setup that would definitely affect how the car runs.
Please post pics of the hose routing when you get a chance.
Thanks, Jared