You will need allen wrenches (seat collar, seatpost, stem) and a 15mm wrench (for the wheel bolts). Usually, allen wrenches come in sets so you should have a variety of sizes, though you'll only be using 1-2 primarily. You should also make sure your bottom bracket and cog/lockring are securely tightened (may need a lockring tool/chain whip/etc for this). My school has a bike garage that offers tool checkouts and there's also a bike collective that has all these.

For the brake, the longer bolt lets you mount the brake on the front hole and you can use a wire cutter to shorten the length. You don't really need to replace the brake pads right away, they should be adequate and you might as well use them. You can replace them later if you need as they get worn.