if this were a 06-08 then you should be ok running it only with the canned trans tune....the fuel timing tables are not touched when you tuned your truck to this level......now if it was the performance canned tune that would be different....
A custom tune is recommended to be used with a CAI due to the maf relocation and the change in the air inlet tube size....
the 04-05's ran lean from the factory....will your 04 have issues? it most certainly could....why risk it????
my best advice if you want to keep using the CTS programming and Cai is to put your stock air intake back on and order custom tunes for the Cai....then order custom tunes.....usually the wait is 4-6 weeks depending on work load...
Or put the programming back to stock and use the CTS as a gauge until the custom tunes arrive....
power hungry performance website link>>>
www.gopowerhungry.com
order tunes for the CTS link>>>
https://fs21.formsite.com/Power_Hung...ure_index.html