Well, I have had a 428 in my '67 Cougar for the last 20 years or so. I've had gear ratios of 3.00, 3.25, 3.75, and 4.11:1. I've had two engines (three if you count the original 390), had 3 (four if counting the 390) cams and 3 (four) different stall converters from 2600 rpm to 4000 rpm. I've had tires from 26" to 29". I've had a wide ratio C6 and and a two standard ratio C6's. I really know this car like no one else. I've run dozens of timed 1/4 miles (on the G-Tech, sorry Tommy!
) I had two 3-speed stick Cougars before that with 351W's and 2.75 and 3.00 gears. All I am getting at is that there is wide range of good combinations you can have. The amount of variables is such that you would need to use multivariate analysis to really sort it out. Short of that, I think you need to look at just the variables that you know for sure. Each decision that you make will affect the next one.
For instance, you pretty much know your displacement and weight. An over-bored 428 and an approximately 3500 lb car. You mentioned an rpm limit of 5500. I think you could raise that to 6000 and still not worry about longevity or reliability. You mentioned not being worried about using highway gearing. To me that means you don't need a 2.75, 3.00, or 3.25:1 rear gear. Since you want to keep the rpms reasonable, I think that means you also don't want a super low gear like a 4.33 or 4.56. So I think your gearing will be in the 3.50 to 4.11 range Your call, but that is what it sounds like to me. You also mentioned 91 octane. All these things seem to be fairly set.
To me it sounds like the next two questions you have to answer are:
(1) what heads you are going to use, and
(2) what specific tranny you have, and what rear gear you want.
I vote for the TFS heads. I haven't run them, but man have they had some impressive results posted here. Money well spent, in my opinion. How much gearing you can live with is very subjective and dependent on what transmission you have, too. More gear equals more possible cam and more possible rpm and more possible power.
Once you have answered those two (and a half) questions you can move on to the next ones. That might be cam, compression, intake manifold, and exhaust.
So what heads? What trans do you have, and what rear gear do you want to use?paulie