edge/gryphon custom tunes?

[20045.4x4]

HI, I'm new to here and had a couple questions. I'm looking at buying a used edge for my 2004 f-150 with the 5.4. I've been told that running a CAI and having the stock exhaust with straight pipe and rear cat delete could cause issues. So I'm thinking of sending it to PHP and having them do a custom tune so I can still run my current exhaust and Intake. I live In BC Canada so i'm just kind of worried if it doesn't work for some reason it could cause a big headache. Thanks!