I prefer Edelbrocks for stock stuff or mild performance applications. They're easy to adjust, seem to get better gas mileage, and keep their tune well. My experience with the several edelbrocks I've used has been that most of the time you can bolt them on, set the idle, and go. I've never had any problems with bogging, hesitation, or air/fuel mixture. That beig said, I've never seen any winning hardcore racers using edelbrock on their racecars. Holley would be preferred for a more performance oriented application. Holley's have a nearly infinite range of adjustment, so if/when you get it dialed in, you'll be good to go. Sometimes they work great right out of the box, other times you have to spend some time tuning to get them to work right.
In your situation, with a 69 Mach 1 and a 428 CJ, I'd stick with the stock 735 holley, or a generic replacement 750 Holley, you won't notice a difference in performance when either is tuned properly.
And, 3.25's seem to be the best all around gear for frequent highway cruising, while still having fun at redlights. With all that big block torque, you won't notice a performance difference between the 3.25's and 3.50's, but the rpms will be more comfortable on the road. 4.10's is definatley too much for a highway car without overdrive. In my 65 F100, I normally run 3.25's, and with a 28" tall tire, they're fine on the highway. I have a 2.47 geared chunk from a Lincoln that I swap in for occasional long distance freeway trips(i.e. Power Tour). In my 66 mustang, I used to run a 3.25 chunk and it was fine on the highway with 26" tall tires, but it was a little buzzy on the freeway going 75 mph, the overdrive and 3.70's fixed that though.