Complete Audio System Upgrade

Hey everyone. I'm hoping someone has run into this issue, or knows what the hell I need to do...lol.
Initially, my 2014 Platinum had JBL system. I replaced all the door speakers with new JBL, put in a new 10" sub/enclosure, installed an aftermarket amp (Rockville 5 channel), and installed an inline processor and connected to factory amp (since I was keeping stock head unit). In a nutshell, system still sounded like garbage, and I figured it was because of the stock head unit.
Two years later (current), I finally bit the bullet and bought the Alpine ILX-F511.
I purchased the wiring, harnesses , maestro, etc...(plug and play kit) from Crutchfield for the HU.
I took out the inline processor, removed the factory amp (capped any loose wires that were cut), ran RCA cables from head unit for ch 1, 2, 3, 4 (single for each channel), and a set for ch 5 (sub), and also ran an amp power-on line from head unit to the amp.
I'm only getting sound out of driver side front and rear door, and slight sound out of passenger front tweeter. Nothing else soundwise on right side, and nothing out of the sub.
I've checked speaker wire connections at amp, and swapped around RCA cables at amp. I can't get this figured out .
Did I Fk something up by cutting out the factory amp completely, when possibly some of the plug-n-play is wired for the factory amp being left in (even though I selected aftermarket amp option when getting the wiring kit from Crutchfield)?