I suggest trying the stock H pipe one time at the track, with the good suspension parts, and sticky tires, and just see.
I went to the track a few weekends back and my big shiny new off road X pipe didnt do f%^k all for my MPH and definitely did kill off some low end torque to where leaving at 4800 RPM on a 5 speed car w/ 3.73s [2.95 trans] the car would dig in, jump up fer a sec and lie down then go. You can see it on the tape every time I launch the thing.
Last year, I ran 1.84, 13.11 @ 102.74 MPH [& best 60 last year was a 1.78 spinnning some on stock suspension] with my Mac equal lengths, stock H pipe, striaght pipes and tails.
This year went 1.77, 13.14 @ 102.95 MPH, with Mac equal lengths, Off road X, magnaflow straight thru muffs and tails.
I think it was only able to run the same ETs BECAUSE I had the suspension work done...
Weather conditions were smiliar.. track condidtions were similar. On a stock heads/intake/cam etc car, too much exhaust stuff IS overkill in my opinion. At least on my car. If it would have been worth the 10 or so HP over the stock H I would have at the very least went 103.0000000 MPH and didnt. [boy did I try LOL

].
Willys - If you car were mine... either a 28" slick to compensate for the gear, or go back to 3.73s, and try the stock H pipe out at the teack one more time and see. I think you'll be happier. IMHO on a stock heads and cam car, if you are up around 4800 RPM approaching the traps the car isnt doing a whole lot except spinning a bunch of parts because the HP is done and over with by then. Just my thoughts based on what I have seen in a buddies 90 LX w/ an auto. Took very little to go 13.70s - 80s @ 97 MPH... Did have a 3.73 gear and 27" tall Hoosier DOTs.