2. Exactly (there is really no way to improve things). The RX rally car notes from Subaru show where they ported. They basically just worked on improving the short turn radius, but even if you blend it as best as possible, you're going to get massive flow separation right where the throat meets the seat. A wet flow bench with some UV dye in there would be good for a few laughs. You'd see fuel wetting out in a massive way and huge cavitation on the short turn side of the valve.
The main area where things aren't what they seem (where flow is concerned) is in cross section vs flow rate. Bigger is not always better. As far as shapes go, regardless of cross section, for non-turbulent flow (intake side), straight is best and equal length (port roof to port floor) is best (straight is equal length of course ... but you can also get equal length by turning a "C" into an "S" ... impossible on a flat engine tho). Any and all deviations from this require additional flow energy (i.e. a reduction in volumetric efficiency) due to shear. You don't need a flow bench for that part of things. You can actually just section a mold of the port to create a cross section profile then "back out" the velocity numbers from that. It won't tell you everything tho.
You DO need a bench on the exhaust tho, as I'd bet one would find massive gains there by building up the port divider all the way to the flange, reducing overall cross section, and turning the siamese into two much smaller ports. It'd be very difficult to know without numbers tho.
3. I don't think you need as much money to make "big" power (in EA82T terms) as has been claimed. If you took care of the heat issue FIRST, head gaskets, head studs, forged pistons, etc simply become redundant. Take care of the heat issue and you won't have the expansion/annealing problems that contribute to gasket failure (walking heads) and head bolt thread pullout (weakened aluminum). Knock will also be greatly reduced thus eliminating ring land failure. Suddenly you don't need studs, MLS gaskets, or forged pistons. Head cracks won't be a problem either, especially if you dump the log manifold and go to a TD04L or larger (HL perhaps) exhaust housing on the turbo (with a nice downpipe and exhaust system). Later spool is good for decreasing knock ... and making power up top means lower peak torque which rods and cranks tend to like. Slightly less torque at higher RPM can really reduce peak loading on the internals. Opening the exhaust yields more power at the same given cylinder pressure (easier on head gaskets and head bolts) as you get a better scavenge effect (higher VE, less combustion endgasses left in the chamber) and thus a better burn with less fuel and less boost which results in less knock too. More complete burn from not having to run pig rich all the time increases mileage and decreases EGT as you turn more potential energy into pressure and less into heat.
Oh, one other neat trick for solving the head gasket and knock problems. You can mill a "ring" in the deck in the aluminum around the bores. I haven't looked to see how thick the closed deck webbing on the EA82 is (should fish out my spare block and take a peek), but if you could put a 3 mm ring all the way around the cylinder, this would massively reduce peak temperatures in the top of the cylinder and probably lead to near infinite head gasket life. Lots of sleeved and/or deckplated builds that were originally open deck incorporate this trick to retain the advantage of that design with the added stability provided by a closed deck. This would be like $50 bucks of machine work on the block. Not expensive. One can also do some radiusing on the oil and water pump and block passages to improve coolant and oil flow substantially. I did this on my current EA82T. Took an hour or two of my time (so basically free).
Here's how ERL does it:
http://www.erlperformance.com/honda-k20-erl-superdeck-i-sleeved
To what the O.P. wants:
1. Get a hugely "oversized" radiator
2. Uncork the exhaust and get rid of the log manifold (your heads will thank you)
3. Don't rely on the knock sensor to pull timing. It can only react. Set your ignition so you don't get knock (pistons will last forever). Use good gas.
3. Intercool and oil cool (less knock, more timing).
4. Do it all on a freshly built longblock where you've had the heads and deck surfaced (fresh surfaces combined with proper cooling ... the head gaskets will not give you a problem)
Then if you want more power without upping the boost, there's a lot to be found by spending a few minutes on a few specific areas of the cylinder heads. They'll still be junk, but much improved junk. Also, spyder manifold swap will yield horsepower at higher RPMs if you have done the heads (if you haven't, the heads will likely choke flow before the OE intake manifold).
The head gasket problem is a symptom.
Cracked ring lands are a symptom.
Cracked heads are a symptom.
Solving the underlying problem is not that expensive. Get exhaust heat out quickly. Get coolant heat out to maintain T-stat temperatures under load. Get oil heat out for the moving parts benefit.
To make more power, don't start with boost and timing. Those two come last. You add boost to a healthy engine with overhead ... rather than trying to make a modified engine healthy.