Sounds like it could possibly be a charging issue, but maybe not. is the 100a alternator of the "1 wire" type? It may not be making anywhere near it's rated output at lower RPM. A pair of Taurus fans should only be drawing 40 or 50 amps. You really shouldn't have any problems with the ECU until the voltage gets down in the 11.5 v range. Where do the fan relays get their power from? Aftermarket EFI systems are often quite fussy about where they get power and ground from, and also where the ECU is mounted. It has to be as far away from electrically "noisy" devices like coils, ignition boxes and even electric motors(like fans).
77 Vega Estate wagon- project(someday)will have TPI305/T-5, S-10 spindles/axles
72 Vega HB Drag Car -383/'Glide/9"(email@example.com)(firstname.lastname@example.org 1/8th)
76 Vega GT- 400/4spd/9" retired from active duty(rusty)
03 Silverado 2WD ex.cab (work truck/parts hauler)
04 Silverado 2WD ex.cab (retired)
06 Haulin' 20ft enclosed car transporter
93 Suburban- 350/4L60(retired)
00 Saturn SW2- wife's car
01 Saturn SC2- younger son's project
00 Saturn SL2- daughter's car
98 Saturn SW2- spare
and 3 more Saturn "parts cars"
Note- the very act of listing all of these has made me realize I have some kind of problem.....