Just make /fly an enchantment that can only be put on boots. Or make boots that have /fly on them. They're permanent until broken, lost etc. And they should also be fixable.
Fly notes are unreliable and a scam. You're paying 50k for 1 hour of flight, you're lucky if you get 10-20minutes, Either you'll accidentally /warp some where, accept a tpa request. Or the server will crash and there goes 50k.
Making /fly an enchantment item does not infringe any ranks ability to acquire it. It's not against EULA rules.
For /fix. I was playing on this server were all you had to do was left click an anvil and it would fix the item (The anvil will still take damage, and it would still cost 1 level, and diamonds depending upon how badly the item is damaged.)