Percussion I would use a stereo Royer SF-12. The last album I worked on I recorded bongos, congas, acoustic guitar, and ocarina with this mic and it worked beautifully on all of them.
Flutes and such I'd use a Royer 122 if it needs brightness, or a regular 121.
Loud stuff, yeah an SM57 would work, but maybe try a padded Schoeps MK5, MK6 or MK41 capsule. I also own an AKG C5 which beats an SM57 on certain things any day - it's like a dynamic mic but uses condenser technology.
Large diaphragm condensers will sound good on the strings - though I prefer Schoeps myself. Also, ribbon mics sound great on strings to get a warmer sound.
But, more important than the mics I think is WHERE you record these instruments.
If it's a regular classroom with hard floors, parallel walls and a large blackboard/marker board with tons of windows, your acoustics are going to work against you.
Find a nice, deadened if possible, but if not deadened then find a smooth echo which doesn't zing or bounce all over the place - especially the loud stuff.
Maybe he knows of a studio you could use nearby... It would be well worth it.
Also, sampling instruments and recording things "for the sake of getting them recorded" is actually a highly specialized field of recording which is much deeper and more involved than having the person run through a musical scale once or twice.
I recently recorded a grand piano and we spent 2 weeks at 8 hours a day recording every possible midi velocity and note and keeping it in tune and perfectly recorded. And we didn't use a person's finger on each key - it was a hammer which would hit exact velocities each time for exact accuracy. You might want to read up on how they record sample libraries - might be useful data for you there.