You need to get some sticky tires to eliminate tire spin for a true and fair comparison. Footbrake it to 2000 rpm, shift at 7000 (or better leave it in "d" & command the trans to shift at 7000).My first run I shifted at 6700 second run I shifted at 7000. It picked up .10 in ET and .5 MPH. Backed up 3rd and 4th runs.
It's as fair as it's going to get. I got a tiny bit of tire spin with the truck mani and none with the mustang mani.You need to get some sticky tires to eliminate tire spin for a true and fair comparison.
Or just downshift a gear or two and let it sing.0-60 is as much a test of available traction and driver skill/method as it is torque output. Tough to put too much stock into these results.
Also, as you are finding, each manifold will have specific tune requirements, so unless you go all out and complete the tune for each manifold, the results are not a true comparison unfortunately.
in the end it makes perfect sense that the F150 manifold would feel better down low, but I have a tough time imagining it to perfrom better at WOT acros the entire RPM range.
All that said, the right solution to this problem is to go buy a 392 Scat Pack If you want low end torque, they have it in droves. ONLY thing I miss about my SP is that low end torque. ..
Now would be the time to do it...Been doing some normal tuning type stuff with this "truck" manifold and it responds well. I may take it back to the track. I found 15 more pounds of air at 6800 with minor changes.