svbc

I recently installed a megasquirt pnp2 from DIY auto tune on my 94 1.8 Miata. I got it all installed and set up for first start. It cranked and barely ran for about 5 seconds then let out one helluva backfire and died. I had my timing light hooked up but found out that it is broken. I'm just wondering if this is a typical first start or if it should have fired and ran a little better. I also noticed that after I turned the key off and back on the check engine light flashed twice for about 5 seconds and then went solid. I was under the impression that the check engine light wouldn't even come on with the megasquirt. Is the ecu trying to tell me "hey you screwed up dipsh!t" or is It normal?