You never mentioned how old your engine is, condition it's in, it's piston types, i.e: forged, cast, H.U. ,
what cam profile, and does it mate well if you did put a supercharger on.
If the tech know everything about your engine from what you told him, then I would weigh out downtime if you did pull the engine to stroke it first vs. your budget.
Versuses just the supercharger done now. Improved heads are something you might want to invest in also if you just go the supercharger route.
IMO, I like to do thing just once. So if stroking it is your goal, pull it and start collecting everything you need. In summary, it really all comes down to what you would really like and what you can afford.