Check engine light flashes, goes off

When I bought my WR250R, the check engine light was just on all the time (EXUP valve removed, FMF pipe, header and programmer were installed). Today the light was flashing (~1 second blink) and sometimes when riding, it goes off altogether. It appears at all throttle levels, all rev ranges with no other symptoms. I don't think the light was burned out because it still comes on when I turn the key. The bike is a 2008 and I don't know if the fuel pump has been changed so that's a possibility, but I haven't experienced any stalling of hard starting. I just changed the chain yesterday (previous was a terrible standard chain, new is DID X-ring) and I just adjusted it per the manual. Any ideas? Should I be carrying around a spare fuel pump perhaps? What can trigger the light? Thanks!