Anyone else using MegaSquirt on a LA motor?

Unlike mentioned earlier by someone, the Lean Burn distributor is a good match for digital ignition, because it was designed for it by the factory.
Rotor phasing is not an issue.
You only need to set the baseline trigger/timing once, so the balancer/crank and Megasquirt timing are synched and actually match.

Also don't just lump all ground wires together, or don't take short cuts and think it's fine.
Read and follow the manual. It's a tough cookie to digest when most of what you read is new information for you.
Grounding is very important to be done properly and prevent stray currents.

You can test-run your engine with just the HEI-7 or 8 module only, just to see if that part of the ignition system works properly.
The module will run in non-bypass-mode and take care of (fixed) timing and dwell.
Once hooked up to the MS, the HEI senses this and hands over the ignition control to the MS-ECU after 5 seconds of engine runtime.

For some additional info, I had some occassional noise spikes and turned on noise filtering in TunerStudio.
Not sure how much filtering-options a MS2 has, but the filtering seemed to have removed the noise all together.