does the custom software have dlls etc in the system folder and entries in the registry? If so, can only suggest you try rebuilding it elsewhere by, for example:-
Copying the Program files folder to other machine
Run the executable - it should return dll not found or similar. Copy that file from problem machine to other machine, & repeat till it stops complaining about missing files. It may now run - creating its own registry entries - or it may just fall over - because of lack of registry entries. So, you'd need to find the registry entries in the problem machine's registry - eg, by loading the software hive from \WINNT\system32\config on the original machine into regedt32 on the new machine, finding the appropriate branch (hopefully under program or supplier name), and exporting it - so you can import it to registry on new machine. This sort of approach was also what I meant regarding removing the problem drivers - except you'd actually update the problem machine's - presumably system hive in that case.
Just some ideas.