As the OP mentions swapping over sensors, I took it that he wants to fit an earlier engine but using the Thor ancillaries, so effectively making a replacement engine but using an engine from a GEMS car as the basis. In which case, he would still be using the original Bosch ECU, just swapping the mechanical bits.
The change to Bosch Motronic engine management was nothing to do with BMW, they'd owned Land Rover since 1994, it was due to the GEMS engine management being sufficiently OBD compliant to keep the NAS regulators happy when it became mandatory in the US in 1996 but not sufficiently compliant when OBD2 became mandatory in Europe in 2000. Hence the change in mid 99.