Backfires 1 time (in the intake) runs about 1 second and then stalls.

Hi all I am having a fit with a 2005 sportsman 500ho efi. The starter spins the engine over just fine. When the ignition fires the engine backfires (at the intake) then will run for 1 or 2 seconds and stall. A little history. I have replaced the timing chain, gears, guides and tensioner 6 mo ago. Along with that repair I replaced the piston and rings. The valves sealed off well at that time so no head work was done. It was inspected by a machine shop. We have driven this vehicle daily working a deer lease. Two months ago the vehicle would not start (dead battery) so I tested the system and replaced the stator and with it came a new pick up for the ignition system. The stator had 2 burned coils and was definitely bad. Five days later the battery was dead. Tested the battery and checked ok, tested the charging system and it was not charging. After some inspection I discovered the regulator was defective ( I is part of the ecu) so I replace it. After I put it on the charging system was working again. I looked (after I put it all together) at the connections on the defective ecu and saw some of the pins were black and burned looking. I will go tomorrow and pull the ecu and re-inspect those pins for discoloration. Is there any thing else to check? Oh I have pulled the cam cover and valve cover to look at the valve timing and valve adjustment (both look good).