code 41 (EST open) now what?

I am looking for help with an intermittent issue I'm having with my 94 Caprice Wagon.  We drove from MN to FL on vacation a few weeks ago, 500 miles from home the car developed a misfire at and above 3000 rpm.  I limped the car all way to FL, drove it around all week (skipped picture spots of anybody saw my other post) and made it home.  If I kept the RPM below 3000 all was fine.  So I got home and replaced the Opti with a Summit unit, replaced the cap and rotor with a MSD unit, replaced the plugs and wires and installed a MDS 6A box.  It runs fine and all seemed fine, I can rev past 3000 rpm but it will intermittently run poorly.  Its hard to explain but the issue is at the top of second gear at WOT, at 5000 rpm its starts missing and wont shift into third until I lift a little (speed is 80-90 MPH by this time) then it will shift to third but then it bogs down until I lift all the way off the throttle, I can then go back to WOT and the motor is running fine.  I replaced the TPS and checked fuel pressure, pressure was low at idle so I replaced the pump, strainer and filter pressure is good but the intermittent problem is still there.  Most times it will run up to about 5200 and shift to third with no issue but other times it just lays down at the top of second.  I have a ALDL cable and EEhack and its showing code 41 (est open).  Where do I go from here?  I cant really find what code 41 is, is it the cam position sensor or the crank position sensor? Im new to EEhack so any tips that can help me troubleshoot this is welcomed.  Please help.

Code 41 shows the PCM is not getting the correct crankshaft position information. Generally a sensor problem, but can be due to a connector or wiring issue.

ok so I was able to clear the code 41 and it did not come back. Now that I think abut it that code must have come from the first start attempt after eh MDS 6A install, I unplugged the factory ignition module thinking I did not need it but the car did not start so I plugged it in and it all was well. So I seem to have no trip codes but still have this intermittent issue. 95% of the time it runs great.