long boot time fixed by flashing boot manually
I have experienced the 'long boot time' with the omni logo showing up but not doing anything happen. tried clean install, formatted data system partitions/ factory reset nothing worked.
Finally, I went into fastboot and flashed the boot.img manually
and the system booted up in matter of seconds. (The boot.img was extracted from the ROM's zip posted in OP).
After the phone booted up fine, I went back to TWRP 188.8.131.52 and flashed gapps-minimal and the reboot was a breeze too (matter of seconds).
I am coming from stock 4.1.2.
Thought this would help someone stuck at boot logo (omni).
and, thanks OP. its a day old that i am on the july 1 build and things seem to work okay so far!