Bypassing the JBL amp 2010 non-nav

I upgraded my HU last spring with a Pioneer 4100NEX (using with Android Auto), and I am not very impressed with the system sound quality. I would like to try bypassing the factory JBL amp that is under the passenger seat, and just using the built in amp of the HU.

I am also considering a speaker upgrade at the same time (definitely front, maybe rear). I was thinking of set of 6-1/2" components like the Infinity PR6500cs (woofers in the door locations, and the tweeters in the dash locations). These speakers use an included crossover.

So my questions are:
- To avoid running new speaker wire to the doors, would it make sense to try running wires from the Pioneer HU down to the area under the passenger seat, and then tapping into the wire harness that feeds to the existing speakers? I found a cheat sheet that shows the connectors on the JBL amp (attached). There is a separate + and - wire for each of the 8 speakers.
- If I did do the above, and I used the speaker setup mentioned above, I would only need to run one signal to the front corners, since the signal from the HU would feed the crossover, which then splits the signal into the woofer and tweeter?
- And if I didn't update the rear speakers (yet), would the the squawker and woofer need to be placed in parallel to work correctly? In other words, LR+ output from HU connects to both the squawker LR+ and the woofer LR+, and LR- output from HU connects to both the squawker LR- and the woofer LR-?
- By taking the factory JBL amp out of the system, will I lose anything? I see there is a mystery Instrument Panel speaker mentioned in one of the wiring diagrams. Is this the speaker that creates the tone for some of the system sounds (alert beeps like the low fuel and seatbelt chimes)? I am attaching the reference diagram with this also.

EDIT: I used to the Metra Axxess TYTO-01 to interface the Pioneer HU with the factory wiring and JBL amp.

 

I should add one more thought. Perhaps try updating the SPEAKERS before attempting to bypass the JBL?

From what I have read here, the factory speakers are all 2 ohms? So will the Infinity's I mentioned in my other post be a problem if they are listed at 3 ohms?