Sounds like you need to hook up a diagnostics computer to yer truck. If you want to do it yerself, you can buy something like AutoTap, DashDyno,

Are you sure the bulb to the check engine light is still working?

Things that it could be...
TPS, Engine Coolant Temperature Sensor, Fuel Pump, fuel filter, thermostat are few that come to mind. <img src="/forums/images/graemlins/wink.gif" alt="" />

Are you sure you don't have an air leak from the ISR mod?

1998 T-100 Xtra cab SR5 2WD Auto; Roadmaster Active Suspension; Yokohama Geolander HT-S; lowered air dam; full belly pan; 4? diffuser; 11" side skirts; dual transmission coolers; 67% grill blocked; Auto-RX'd; ScanGauge II/Ultra-Gauge