Locked out of my current Apple ID purchases

I just got my iPhone 6 Plus and I recently signed into my old Apple ID to download some movies. Now, when I go back to my current ID it says "This device is already associated with an Apple ID". What is going on? and why would I have to wait 90 days? I'm a HUGE music geek and NONE of my songs are showing on my iPod.

If I back up my phone, then restore it through an iCloud backup, set up a new ID and re-purchase iTunes Match through the new ID, will all my apps still be there? and will it be fixed?