well, I'm not brad, but I'll see what I can do
1. Personally, I think the 3L heads are a better choice (over the 2.5L SVT heads) in most possible configurations of a 3L in an SVT (or non-SVT for that matter) for many reasons. The only real advantage of the 2.5L heads on the 3L block is a big jump in compression ratio. This can be a mixed blessing; it will help to make more power, but at the expense of much higher likelyhood of detonation due to the higher CR, as well as the effects the 2.5 head has on the squish band (several effects are involved there, and though I don't quite understand all of the stuff going on there, one thing is the increased likelyhood of hotspots that will contribute to det.)
The 3L head also comes with larger valves, allowing for increased flow into and out of the cylinders (SVE considered adding these larger valves for the 2.5 also, but cost and already having met the power targets kept them from doing so)
2. Any "factory calibration" will not be optimal on any modified engine, let alone a heavily modified one. A custom DYNO-tuned chip will be the best choice in most cases. Also note, the stock fuel system is not likely to be up to handling a modified 3L. larger injectors, compensated for in the ECU, or increased fuel pressure are likely to be necessary to feed the beast.
Honestly, If I was building a 3L right now (unfortunately I'm not in a position to right now) I would get an 01+ long block, balance and blueprint it (if I could afford it) port and polish the heads (I would at least clean them up a bit) use the cams from the SVT (or the unobtanium SVE cams that David Z managed to get)
beyond that, I would go with a heavily modified SVT upper intake manifold (Terry is working on something right along the lines of what I am talking about) a 65mm TB, 70mm MAF, headers and a 2-2.25" true dual exhaust w/ an X crossover.
Note, nothing but the intake manifold is really unobtanium or expensive from what I just mentioned is Terry's intake manifold, which hopefully he will make available after he finishes development.
