1st. Make sure you have the newest d2lte build from Philz flashed. If not, flash it. Also, and this is just the way I do things. I use the reset to install new ROM option in Philz, wipe cache and then wipe Dalvik. I then flash the ROM. Then, in Philz I use the reboot recovery option and boot back into Philz. I then flash my GAPPS and reboot. I wait until the ROM is set up before flashing the APN fix zip. Been doing it that way for awhile with no issues. Sometimes flashing too much at once can cause problems. Also, when it comes to a kernel, I always flash and set the ROM up, boot into Philz and make a backup before flashing a new kernel.
Just wanted to share the steps I use. It's the safest way to flash the ROM and GAPPS together.
Some of the AOSP ROMs have been having issues with PA GAPPS. There was a pretty recent update to PA GAPPS not long ago. I updated my PA GAPPS and haven't had any GAPPS issues. I've probably flashed 6 AOSP ROMs with the newest GAPPS.
I got that message in Philz about wanting to overwrite something. I did the same thing you did and the phone bootlooped. I went back in and went through my flash steps and allowed it to make the changes the 2nd time. The phone booted up fine. I don't know if the ROM required Philz to modify a folder or not. I took the chance and it worked for me. Should work for you as well. Whatever the change it needed to make, you don't have to worry about losing Philz.
EDIT:
Just a heads up on a new ROM that's out that I've been running for over a week now. It's called Bliss Stalk and is based on the BeanStalk ROM. Bliss has been running great for me. I've got the OmniSwitch activated and it's working fine. Once in a while I'll get a pop up saying Omni has force closed. It's a false warning. I've actually been using the OmniSwitch when I got the force close pop up. Omni didn't even crash and kept on working just like it's supposed to. OmniSwitch works fine.
If you would like to take a look at the ROM, here's the link-
Bliss Stalk-
http://forum.xda-developers.com/showthread.php?p=56215406