Great News
Gotta love that feeling when all that work starts and fires up the first time! Congrats, and have a beer! <img src="/forums/images/graemlins/cheers.gif" alt="" />

I would try experimenting with
Trigger angle "addition" by 10 degrees at a time to try and get Megatune and the timing light to match. If it wont maye change your base trigger angle to 50 (or 70), reset the "addition" to 0 (ZERO) and try again etc etc.

I am working on finding a base map for you, (in VEX format) but you may just have to manually edit all 144 cells (it's really not that bad)
MAKE SURE YOU READ THE MEGAMANUAL AND MEGATUNE DOCS ON TUNING
basially
Just have someone drive at steady road loads and on the laptop in Megatune navigate to "live" VE map tune screen, observe O2 (V>450mV=too rich OR V<450mV too lean) and press the G-key to allow the editing curser to automatically "follow" the engine within the current cell then just press Shift ^ up arrow to go richer or Shift ^ down arrow to go leaner (based on your 02.) You dont need to "hit" every cell, cuz you can do a little manual blending afterwards.

Keep pressing the arrow key until you can get an O2 swing to the other side of 450mV THEN STOP work back a couple key presses until it "just" flips ABOVE 450mV (in that cell) so now you KNOW you are richer than 14.7:1 (of course a wide band O2 makes this step a whole lot easier- ie O2 targeting)

Same process for the timing advance basically except it's alot more dangerous as you add advance under boost. I'm working on adding a GM knock sensor system to the MS and hope to have it done in the next couple weeks- something I'm sure you'd benefit from, so I will advise when I get there. (BTW Roger Ennis' Palm Pilot tuner works now in MSnS-E, so if you have one...)

My congrats again, you've successfully broke new ground when it comes to MS and MSnS-E THANK YOU AND CONGRATS!!
(Hopefully we can convince the masses that you dont need to mount a 60 tooth wheel and run Ford EDIS to make MS provide accurate (and more important "tunable) spark timing.

GJ <img src="/forums/images/graemlins/smile.gif" alt="" />
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