Indeed it should be pretty easy to add an external FPR and leave the stock one in place. In theory, if the rail pressure exceeds it's set (or failed-to) pressure then it will simply fully open which will allow the external FPR to be in control of the fuel pressure. I'm not sure on how to gut the internal regulator yet, but as long as you keep the top cap straight and the body that holds the O-ring that's all you need to keep it sealed.
I myself have resorted to telling my ECM what my actual fuel pressure is, as long as the duty cycle of the injectors keeps up with fuel demand at a lower pressure in and out of PE.
As far as fittings goes, the return line is 5/16". Earl's has fittings that fit onto tubing and tighten to them using compression ferrules (rated to 250psi). They have them go to -6an size hose (3/8") which would then be easy to plumb to wherever your FPR will be mounted.
I have a full parts n pieces list in a thread I started:
AEI-13129, FPR, $141
EAR-610006ERL, Hose 10', $66
EAR-AT165056ERL, Tube to hose AN, $11 x2
EAR-AT949006ERL, AN to FPR, $16.95 x2
Total to upgrade: $263.99
The AEI FPR will boost reference above 0 vacuum, so conviently that FPR will work for you, as long as the fuel pressure you intend to run is <70psi (it's advisable though that if you want to run 65psi that you get a FPR with a higher max setpoint to allow it to more smoothly control fuel pressure transients).
Clear as mud ?
As far as the manifold goes, from what I read on FSC the most restrictive part of the intake is the internal baffles made into it. Of they're cut out you have more flow, but lose runner length. The only way to cut them out is mill them from the bottom then tig the casting closed... which no one that I've met on the webs has done yet.