Tuning is easy if you do it in steps.
First step is simply getting the engine running. It is far easier to tune from rich to lean than lean to rich. Lock out the timing on the timing table (or there is an option under ignition that says "fixed timing" or "Table" and set it to fixed, to like 15*). Set the required fuel value based on your injector and engine sizes (it calculates it for you with that information).
I like to set the lower left corner of the fuel table to a flat 30, then the top right corner to 100 and use the interpolate tool from about 2,000rpm up and 50kPa up. Then fire it up. You'll probably have to pedal it some to keep it running, but as soon as the AFR's start reading you'll be able to tell if you need to increase or decrease the 30. Once it is at a stable idle at a reasonable AFR (like 13:1 to 14:1), let it warm up to operating temperature. It may lean out as it warms up due to the warm up enrichment turning off. So watch for that and richen it up as needed to keep it running. While it's warming up, check the timing with a timing light and verify it matches what the MS is commanding, if not make the necessary adjustment to the Trigger Angle until it matches.
Once warmed up, you're ready to tune. You may need to adjust your kPa and RPM bin's to match your engine's operating range. I have no problem sharing my fuel, spark and AFR tables, but understand the kPa and RPM bins may need shifting. For reference, I started my Firebird up on my Skylark's 455 tune, lol, then adjusted from there.
When in doubt, the MS3 has very quick AFR correcting abilities, so you can technically turn on the EGO corrections, set the controls to a lot of authority and come on at low temperature and it'll meet the AFR's you specify in a table. That can get you driving fairly quickly, but is a LARGE crutch. I may of done that to get my Firebird driving shortly after start up =)
Back to tuning, it's pretty difficult to hurt the engine at idle and low rpm and loads. Get the AFR's working nice with gentle increases in throttle while in neutral/Park. Once there, you'll get a feel for the slope that the fuel table will want. You'll want to turn the timing table back on if you are controlling timing and have a very conservative table, like no higher that 32* for now. Then put it in gear and make sure it keeps the AFR's decent and doesn't stall by adjusting the fuel. Then give it a little engine braking, adjust, a little more, adjust, and that'll get it so with gentle throttle from a stop it should drive nice. From there go for a drive and be gentle on the throttle (don't put yourself in a place you may have to hammer the throttle, like a busy street if you can help it). If you have a helper, have them adjust the fuel as you are driving or you can datalog it and see afterwards where it leans or richens up and adjust it. This will get you a decent tune at part throttle and up to say 3,000rpm depending how you drive it.
Now you'll want to work on the accel enrichment from the AE menu. I use pure TPS when one is available. From an idle, hit the throttle at various rates and watch the dot on the graph/chart. If the engine leans out or *POPS*, move the point up where ever that dot went, if it bogs, move the point down. Once the accel enrichment is decent, back to tuning fuel.
By now you should have a decent idea on the slope of the fuel table and make a decent estimate of what WOT and high RPM fuel values should be. So raise them up to match the slope, then add another five to ten points to it to make sure it goes very rich. Then go out and test by watching the AFR's or datalogging and reviewing, slowly lowering the amount of fuel until you are happy with the AFR at WOT across the rpm range. Then you can start on the timing table.
This process can take a full day or spread it out over a week or two depending how much perfection you are trying to achieve. Even my first time EFI'ing a car (my Buick) I was driving it around town the afternoon of the morning I got it first started.
If you want the MS to control timing with an HEI it can do it in either batch fire mode by simply hooking it up to the pickup coil, or if you want semi-sequential you have to have a crank trigger. If you want full sequential you'll need a crank trigger and modify the HEI to be a cam sensor.
The semi-sequential pairing is fine. And actually, since installing the engine in my Firebird my cam sensor has a fault and isn't reading, so I've been running in semi-sequential mode (it does it automatically when it can't read the cam) since I started driving it. I've been too busy/lazy to figure it out, but I'm suspecting the sensor failed based on my minimal troubleshooting of it.
