This is what I have figured out so far (hopefully correct):
My r300x4 will be my amp for my speakers. So I will get to the stock amp location and the speaker wires should be there for me just to move to my new amp. (correct?). then I will run RCA cables from my amp to my headunit (aftermarket).
My P400x2 will run my sub. I will use the speaker wires to hook it up in the correct amount of ohm(s). Then I will run my 2 channel RCA cables to my RCA Y adapter (to make it one channel) into my sub out on my headunit.
I will be running 4awg power wire and I will bring them together with my power distribution block and run the one 4awg to my fuse holder (with 120amp fuse) ...then to my battery.
Then I will ground my amps and wire the remote to my headunit. *Can I put two wires into AMP #1s remote and run the second wire to AMP #2s remote so that I just run one remote wire to the headunit *
....Also, how will I go about wiring the tweeters since I only have a 4ch amp and the 4ch will be the front 6.5" and the rear 3.5"?
Also any tips on where I can fit my amps? Will I need fans? Any suggestions on which ones?
I would not reuse the factory speaker cables. I would recommend you upgrade your speaker cables. The factory wiring is like 18 gauge or smaller wire if I remember correctly. Some nice 12-16 wire would be much better.
You do NOT need a separate amp for the tweeters and the midbass drivers. They will be able to run off the same channel in the amp. Almost all component speakers come with a passive crossover network. So the wiring goes RCA from head unit to amp then speaker wire from amp to Crossover network. The speaker wire splits at crossover network and goes to both tweeter and midbass driver.
Most head units have stereo sub outputs. You may not need a Y connector to get your amp into bridged mode. Not sure if you are powering 1 or multiple subs with the stereo sub amp.
Power and ground distribution sounds fine. Make sure to find a good body ground and tie everything to it. Helps to eliminate ground loops if the electronics are tied to a known good ground point.
You can daisy chain your remote turn on wires. (Like Christmas lights) No problem with doing that.
I do not think you need to power the small 3.5 in "rear" speakers. They will do nothing for sound quality. You can run them off the head unit if you want to power them up. I have my fade set +7 to the front on my head unit.
Some amps have the ability to run in 3 channel mode. Stereo to fronts, and bridged to sub. That is how I have my system set up with my Alpine PDX amp. Bridged channel runs my Stereo Integrity shallow sub. Stereo pair goes to the front.