Its your call but if it runs good and shifts good and its just the leaking base gasket that is the problem just lifting the cylinders with piston still in the bore would be cheap.
There are many high mileage bikes that have not reworked the heads or pistons.
You would get away with just 2 gaskets and some sealant pretty much.
I myself is worried about the shift drum since I do have false neutrals between gears every now and then.
The rekluse and not using the clutch might have tortured the gearbox over the last 40 000 kms. But now a stock clutch is back in it and will be only street use for the 950 so Im crossing my fingers that it will hold up.
Have changed name, was previously Dirty950