K&N CAI to Gotts mod

[DarkShadowSTX]

Hi guys. I have seen the answer before but I cannot find it right now so I'm sorry if this is a dumb post. Anyway, if I take out my K&N CAI and do the Gotts mod, will my custom tunes still be usable? Right now all 3 of my tunes are for the CAI. I have been noticing my truck kind of bog down with plenty of drone say after 1800rpm no matter what tune I'm running. I'm wondering if that is because of the intake. I never really noticed a performance difference over stock from it ever since I bought it and I'm just looking to find out if I can do the Gotts mod to change things up and get better results.