Can I use a CNC machine or waterjet to make an adapter plate to adapt a 5 speed transmission to a rare, obsolete engine?

A plate between the flywheel housing on the engine and the bell housing of the gearbox would almost certainly be required to mount the gearbox. This would be no problem to produce with a CNC machine.

The problems that then arise would be to reconcile the differances in the two gearboxes.

Will the gearbox obstruct the clutch assembly in any way? Will the gearbox imput shaft engage in the clutch? Will the splines of the imput shaft mate and be driven by the clutch? Will the clutch release mechanism operate the clutch successfully? Will the gearshift lever enter the cab? Will the gear shift lever be obstructed in anyway when shifting gear? Will the gearbox casing fit in the transmission tunnel? Will the gearbox effect the underbody position of things like the exhaust system or fuel tank? Will the gearbox cross member accept the new gearbox mountings? Will the propshaft alignment be in alignment? Will the propshaft connect to the gearbox and allow a sliding joint? Will the propshaft length now be too long or too short to connect to the differencial?

When your vehicle was first built it was with its present configuration. You would need to reconcile each every difference from that first build. In time and expense terms it would be highly unlikely to be a viable undertaking.