We tested the timing light on another vehicle and it works fine. The spark plugs weren't necessarily firing regularly, I just was able to see a strong spark from cranking it over with the plug wire hovering over the intake manifold.
After some more research I think I might know what's going on.
Here's a photo I found on the internet of the 6G72 Crank Pulley.
Ours didn't have an adjustable distributor before we converted it over to the speeduino and I didn't notice those timing marks on the timing belt cover. I was under the impression that the big circle thing was TDC and was trying to get the timing set to that (which is in fact about 10 degrees ATDC by the looks of this picture).
I think the inconsistent timing light is from the rotor being in weird spots between the tips in the distributor cap due to our assumption of where TDC was.
Gonna test the theory tomorrow.