The factory HU has built-in undefeatable equalizer settings to compensate for the interior of the car and the performance of the speakers. If you put a Clean Sweep device between the speaker outs on the HU and the aftermarket amp, it will flatten the output or basically reverse the effects of the EQ settings on the HU.
I haven't tried those Polk speakers before, so I can't comment on how they sound. Listen to them first with some CDs that you bring to see how they sound and see if you like the sound first. I bought some Polk db6750 speakers for another car and the tweeters were a bit too bright for my liking.
$300 is about what I paid for my Arc Audio 6000 6.5" components along with two wood adapters for the front doors. These are some sweet sounding speakers. For that price, you could probably get some Focal K2s or CDTs components also.
Arc Audio's website
is way out of date but I promise you that they make some great stuff. Their Arc subs, XXK, and 6000 components are some of the best stuff you'll find. Even their KS line, that replaced their KAR, amps are sweet. The Foose (FD) and SE are probably way more than you want to spend. The XXK amps are almost legendary for their build quality and sound but they are no longer produced - the FD line more or less takes their place. The KS line is their value line but also excellent stuff.
Are you willing to do your own installation? The wiring isn't difficult, but it can be a lot of work because you have to remove panels and what not. If you've never installed these things before, it might take you two days or so to run the wires. My amp is mounted behind my back seat and a shop mounted a piece of MDF and then the amp to that for $25. The back of the fold-down part is not flat and filled with holes - which is why the MDF is needed. I don't know your plans though. An amp kit from KnuKonceptz
is about $50.
Why do you list a 4 ch amp and a mono amp? Are you getting a sub? If you are getting a sub, you may want to consider removing the rear 6x9s completely because it helps with the imaging from the front speakers. Then you can get a good 4 ch amp and bridge two of the channels for the sub or get a 2 ch for the front and a mono amp for the sub.
Arc Audio 6000, Focal K2, CDT components ~$300
Arc 12 dual 2 ohm sub ~$200 + $120 for a custom box = ~$320
Arc Audio KS300.4 amp ~$300-$350 This amp outputs 4x90W RMS @ 4 Ohms, and 2 x 350W RMS @ 4 Ohms bridged which is enough for the components and bridged for a single 12.
KnuKonceptz 4 ch amp kit plus some more speaker wire ~$65 shipped
MDF plates for the front door ~$30-50 or less if you have some plywood or MDF and access to a scroll saw
Clean Sweep $300
= ~$1400 for equipment if you self install