I used to race in Pueblo...I'm now down near Wichita. Dustin told me for Pueblo & Denver's altitude (not density altitude) .25-.375 smaller pulley on the mountain compared to what I'd run here in KS.
Good luck!
1) Depends. Levittown Ford has best prices I've found on Ford parts. If you don't want to save money and reuse your factory block. Could also source eBay.
2) It seems the Gen3 block stock is pretty good, with a set of drop-in pistons and rods, you might be OK with stock block and no sleeves. If...
I've read a few places of a few people breaking these. I know MMR makes upgraded billet caps, but I'm curious who has broken their stock ones? I feel like if they were as common to break as say OPG's or timing chains, you'd hear more about it.
Having a set of heads ported, wondering if there is...
Having installed the Whipple myself and based on what you described, I'd opt for a Procharger, but you shouldn't let the Whipple install scare you. But my guess is the Procharger install will leave the most stock as the Whipple requires you to modify the factory heater hoses so if you wanted to...
It's been a while, but the instructions say something like taking it one turn, then take it to 6 o'clock or something. I only took it to 6 o'clock. There's a flat spot on the cams, I rolled the engine back over, then re-timed it. I wish I could be more help, but it's been almost 3 years.