Although the 3.50 gears are making you sluggish off the start, there is NEVER any thing wrong with wanting 400hp ;D
This day in age 100 HP per 1000 pounds only makes you a little quick. My bronco has about 325 hp and I totally understand wanting around 400 regardless of what or where your driving.
Definitely build a Windsor. The 1/2 in stroke always make about 100 more foot pounds of torque. Don't bother with a short stroke 302
What '68 Ford says is pretty similar to what my old man told me when I was building my Windsor.
I had 4.11's with 33's for awhile. I thought it would be too low of gearing for the highway. But you really do get used to blasting along at 3,200 rpm to go about 70 mph.
I have since gone to 35's (Thank you Franko) and now, maybe it's 3,000 rpm to go about 70 mph. Didn't make any difference in gas mileage on the highway but the 4.11's definitely helped the 33's get a little better mileage in town though. And the lower gearing made it feel like it did when it only had 30's on it back in the early 80's. It makes a night and day difference off the line.
Now with 35's I really wish I had gone with 4.56's. But I am now wanting to go with an overdrive tranny which will require even lower axle gearing for the overdrive gear to be usable.
And like Tommy said, just do the rear differential at first and see if you like the results. Maybe even take a shot at your own rear gears. The 9" differential is the easiest gear swap you can do.
Anyway, good luck. Lots of good info here.
But generally speaking.
Stock tranny and 33's go with 4.11's.
Overdrive tranny and 33's go with 4.56's.
Older Ford AOD with .69 to 1 overdrive and 33's go with 4.88's.
And just increase gearing incrementally a long with tire size....