So the plot thickens - stock converter on a slipping trans, check engine light is on and haven't resolved the issue, guessing at rear end ratio, you've set the base timing ahead of what the chip programmer intended with an expectation of an increase in performance.
If this was my engine the first thing I would do is verify why the crankng compression is low.
Step 1 would be to confirm my gauge is reading accurately - I'd hook up my compression tester gauge to my air compressor and compare gauges.
Step 2 would be a leakdown test to confirm proper valve and ring seal with one of these :
Amazon.com: OTC 5609 Cylinder Leakage Tester Kit: Automotive
Step 3 - MAKE SURE my balancer is at #1 TDC via whatever method I'm most comfortable with. I use a dial indicator on #1 piston prior to installing the driver side head. But there are other methods that will work with the heads on that are cheap and accurate.
Step 4 is it advance the cam with one of these :
http://www.summitracing.com/parts/hrs-94505/overview/
I would do it in this order because if your leakdown rate is high, then anything else that you attempt in an effort to resolve your low cranking compression will be fruitless. A leakdwon test will confirm that all of your parts are sound and your assembling went as planned.
Once I resolved the cranking compression issue I would now find out why the check engine light is on and resolve the issue. Then resolve the slipping transmission issue and find out exactly what gears are in the rearend.
These steps don't necessarily have to be completed in the order that I would do them in, but you need to start finding answers and stop the guessing. I much prefer to spend a few bucks on a tool or two to identify a problem and spend my money on fixing the issue. The best part is that you'll have the tool to use again - the money won't be wasted.
Regarding ignition timing, if you set the timing advanced or retarded on a computer controlled motor, then remember that the ECM doesn't know that. It, the ECM, is making fuel trim adjustments and timing changes based on the assumption that base timing is correct. Speak to whomever you purchased your chip from and they should be able to explain it fully. Look at it this way, if you advance the base setting 4 degrees and the programmer designed the timing to advance to 38 degrees, then when the ECM is commanding 38 degrees your timing will actually be at 42 degrees and if it begins to detonate then the knock sensor will retard the timing by however much the programmer set it to retard timing which might be 8-10 degrees. This can create a situation where you think you advanced it 4 degrees but the engine might actually be running at 4-6 degrees retarded due to the knock sensor. You'll think the engine is running poorly, which it is, and you created the issue.
Regarding your heads, according to ProMaxx's site those heads are sold with .575 lift capability. If you have a sheet that came with the heads that identifies something different, then I'd call Promaxx to clear up the issue. I would guess that they are setup for a roller as all Vortec heads were orginallt designed on roller motors. But again, I'd eliminate the guessing and contact Promaxx.
Is this process going to take some time - yes. Are you going to have to learn a bunch of information - yes. Are you going to be better for it - yes.
Good luck.