JIS is a must for those tiny screws when you're at the carb slides to change the needle position (if you must).
Replace the 16 crosshead screws that hold the floatbowls by ss allen screws by all means.
Furthermore I have replaced two of the 4 screws that hold the left crankcase cover (sprocket cover) by allen bolts.
For the rest, believe it or not, I haven't changed anything (studs at the headers excepted). Even the chain adjuster lock nuts in the rear are still the ones the bike came with, although now, after hundreds of adjustments, they get a bit round.
An impact driver is an useful tool in your workshop.
I wonder why people change all for allen, it's a waste.
Best advice I ever had, you can read in Zen and the Art of Motorcycle Maintenance. Robert M. Pirsig who deceased last month at the age of 88, tought me about the correct state of mind you have to be in when you do maintenance and when it is time for a cup of coffee.