Kyle,
Let me try to touch on a few of these issues.

1) need to test when the temps are the same -
The temp correction factors in the dyno program should take care of this unless you are running a boosted engine with intercooler.

2) timing - 17 deg is a meaningless figure for dyno tuning.
I assume that you are talking about 17 deg at idle, or at 1000rpm.
You should be checking the timing at max advance. Full advance should be in at around 3000 rpm. The timing should be around 30 - 32 for best power, but this is something that you should try on the dyno. Small changes can make big differences in power.

3) Don't assume that something that works on one engine will work on another.
This is especially bad when you try to emulate on a basically stock engine what works on a heavily modified engine. What works on one will difinitely not work on another. You can try things like carb spacers, etc., but don't assume they are the way to go just because I or someone else said it worked on another engine, with different cam, different head, different CR, different ext., etc.

4) Alum. INtake - the ones that have more material around the opening where the carb is mounted seem to flow better.

5) dyno chart - basically when you see the power dropping off at around 5200 rpm, the point at which the torque and HP curves cross, it means that the engine can't breathe. Either that or there is some other problem causing it not to run well at higher rpms. By " can't breathe " I just generally mean something is limiting its ability to get air in and out. It could be the cam, the carbs, the head, the exhaust or a combination.

John
V-performance.com