You have been taking modafinil for years now and pretty heavily.

I actually haven't. The last of the checklists in the post is actually the one I take the most seriously. I did use modafinil heavily when I was originally prescribed it (for sleep apnea) but now treat that with a CPAP machine instead. I use modafinil occasionally as needed(/wanted).

How have you dealt with tolerance?

I actually have a lot less tolerance for the stuff now than I did when I first started. Even at a third of the daily dose I orginally took I now don't feel tired much for several days. (I can only speculate about why.)

By taking more or cycling usage?

I cycle. Not because it doesn't work but because I need to ensure I get adequate sleep to keep up with the recovery demands of my exercise regimen without weakening my immune system and taking on the features of a zombie. (Bloodshot eyes, pale face. The look people get when they aren't sleeping enough.) I don't like taking modafinil more than once or twice a fortnight.