Can I replace the Subaru EX40 engine in a G300001-G300002 Gas Drive air compressor system with the Honda GX390 Engine?

No.
When Subaru ceased production of their general purpose engines, the VMAC Gas Drive air compressor system was significantly redesigned and updated.

Changes made are both dimensional (base plate & bracketry) and in the control systems.
The Honda Engine does not fit in the G300001-G300002, and therefore will not replace the Subaru engine in those systems.