Stock manifolds/stock Y/Mangaflow/1.25" drop you will be fine. No clearence issues.
If you add headers and a Y, you may run into issues. But it depends on which headers you go with. Kook's, QTP's, and FLP's tuck up very nicely and you will be fine. Everything else will hang and may scrape.
BTW I have Kook's, a catted Y, GMMG and I'm dropped 1.25". I've scraped once in 1.5 years.