I could be an issue with the coding in one of the modules. I had a 210 ch. once where a module was coded for European specs. Caused a bit of random window and sunroof operation but otherwise normal operation. I cant remember which module it was but most of the body's modules have variant coding that need to be programmed for the car. If nothing else it may pay to have the fault codes and module coding checked. I don't have proof but I suspect unintentional coding changes can occur during battery replacement.

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90 300TE 4-M
Turbo 103, T3/T04E 50 trim
T04B cover .60 AR
Stage 3 turbine .63 AR
A2W I/C, 40 LB/HR
MS2E, 60-2 Direct Coil Control
3" Exh, AEM W/B O2
Underdrive Alt. and P/S Pulleys,
Vented Rear Discs, .034 Booster.
3.07 diffs 1st Gear Start

90 300CE 104.980
Milled & ported head, 10.3:1 compression
197° intake cam w/20° advancer
Tuned CIS ECU
4° ignition advance
PCS TCM2000, built 722.6
600W networked suction fan
Sportline sway bars
V8 rear subframe, Quaife ATB 3.06 diff