Your speed sensor near the flywheel could be a bit out of spec after removing and replacing the engine/transmission... you might want to get the clearance measured and re-adjusted. I *think* it should be at around 0.8mm clearance. Best to ask in the Tech Forum.
'89 911 Turbo Cab
Protomotive MAP ECU, Twin Plugged Heads, GT2-EVO CAMs, 3.3L fully finned P&C's, ARP fasteners, C2T head gaskets, Titanium Retainers, Turbo spec valves, springs & guides, 964 splash valves, GT35R BB turbo, GSF Stainless Headers, Magnaflow Exhaust, Full bay Intercooler, TiAL 46mm w/gate, TiAL 50mm BOV, Apexi AVC-R EBC, SPEC Stage3+ Clutch kit, Crane CDI Ignition