ok, more swap issues...

ok, got my 2000 GSR motor into my EJ1, got it running... but now it idles rough on start up (idle goes up and down) but after a couple mins. it levles off and runs pretty damn smooth... but after a little while the car just cuts out, no sputters, just stops running.... no CEL, im running a ODBI P72 ECU and i already moved A20 to A17.... any suggestions??

P.S. the Bat light is on when it runs, so i replaced the Alt. and that doesnt affect anything.