I went back and looked at your photo of your two fuel systems tee'd in on the frame rail.
It's extraordinarily complex, which is fine if you like that, but you might want to start isolating systems before tearing it back down to stock.
Can you run it from a diesel can with a hose to the Holley pump to your filter to your IP?
You might want to run it without the pre-filter just for a drive, just to see if that is clogging and making the fuel restriction. I hate those small pre-filters, and that's why I like the clean-able pre-filter screens that the duralift has. Not only can you clean them, but you can see through them to instantly know if your diesel is clogging the system before it even gets to the pump.
Cut out the regulator and all the parallel circuits. Just isolate the diesel can to holley pump to filter to IP. See if you get the same pressure issues and speed issues.
Well if you ignore the return line stuff, it's not too complicated:
[front tank]-[pre-filter]-[Holley red]-[Racor R26P W/S filter]-[stock filter]-[IP]
I redid the return lines some, so the returned fuel goes straight through the tee instead of turning, and I put a check valve to prevent returning fuel from accidentally going to the rear tank. The branch from the tee and that U turn hose is going to the check valve/transfer pump/rear tank's supply line. I can
probably rule that out as being a problem, unless the tee is too restrictive for the fuel running straight through it. It's not hard to isolate, since I just have to connect two factory steel lines with a 5/16" hose to delete the transfer pump/tee setup.
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The Racor filter head came off of a junk yard IDI pickup with Banks turbo so in theory it should be fine. It was on the firewall in place of the stock W/S. I have the largest micron (30) element on there. It doesn't list a GPH spec though:
https://ph.parker.com/us/en/racor-replacement-filter-element-spin-on/r26p
This store claims 45gph:
https://jwmarinellc.com/product/racor-fuel-filter-water-separator-element-r26p/
Parker/Racor makes (or made?) a drainable W/S fuel filter that fits in place of the stock 6.9 IDI filter. It's listed as 20GPH. I wonder if that's what the Motorcraft FD-811 filter is too, since you'd think they would make the spec the same, since it's exclusively shown as being for 6.9L IDIs.
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I could make the Racor R26p the pre-filter, but I'd have to run a lot of extra hose because there is no other good place to mount it. I have it bolted to the frame where the (missing) stock W/S goes. It's up nice and high, so far less unlikely to get caught on anything I might drive over.
The pic below was with a 2 micron rating element and it WAS causing fuel starving with the mechanical pump.... but it was old and dirty from the truck it came from, so that element was suspect. Not to mention the 35 year old weeping worn out mechanical pump probably wasn't as it's strongest. It would surge randomly under heavy throttle, or something like that. After I got to the next town, I bypassed it and the problem went away.
Hose on the right is the inlet, hose on the left is the outlet.
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So as you can see, it's easy to bypass by just swapping out 2 hose connections, but I seem to recall I tried that already with the new 30 micron filter after the Holley Red was installed. I might have to do it again though, in addition to deleting the pre-filter. Maybe it's a combination of both causing problems. I need to see if I have a long enough piece of 3/8" hose laying around to delete the prefilter. If not, I'll go get some. The pre-filer has been catching some stuff, so I hate to run long term without SOMETHING between the tank and pump.
So.... I guess I'll first try deleting the glass pre-filter and then try the 1 mile interstate run (thank goodness for the extra long on-ramp lane), with the Racor hooked up as it is now, after the pump, just to see if anything changes. That's just a matter of 2 hose clamps and replacing it with a short hose from the steel line from the tank to the pump inlet. That's one of the cheapest and easiest thing to try and like you say, it might be the weakest point as far as the flow. There's a gas station with a bit of semi space due to truck lanes, so I stop there to fiddle with things if I need to after the first 1 mile run, then I can hop back on for the 1 mile run back to the road I started from.
Not far away, I can go on the 2 lane state highway with big hills and not much traffic to further test it, if I end up with good normal top end on the somewhat flat interstate. No point trying that if I can't hardly get to 70+ mph even with the pedal being held to the floor on a relatively flat stretch of interstate.