Well, I'm not a 'pro', but I may be able to contribute here...answers are pretty much in order of your ask...
If you want to replace the speakers like for like (dash = tweets, and so on)... then components are your best bet, and the way to go in that case. More on components when we get to your other questions...
New amp in same space... sure...depending on how big / powerful an amp you want. Since you're not talking subwoofers at the moment, a 4-channel would probably be fine (yes, I know you'll have 6 speakers, with components...no worries). Something in the 200w RMS range would be fine (sounds like you're just wanting more or less a 'like for like' swapout) If you go with a *really* powerful amp, then give some thought to either relocating the amp, or getting some sort of 'squirrel cage' blower / fan for it (which takes up addn'l room, of course)
Since you're suspecting the amp - I think the OEM Bose amps are really starting to show their age - I have one in both my Voy and Sierra, with a 3rd one I got from a forum member...and *all* 3 have an issue (not with the same channel). So I think if you want to stay amplified...get a new one. My .02 on that.
Running component speakers off the HU, instead of an amp... it can be done (just make sure the HU and speakers are the same (almost always 4ohm). BUT - components really 'deserve' an amp to make them sound their best. And (IMO) most people who run components do so because they *care* about the sound quality (you're splitting off the appropriate frequencies to be handled by the right speaker - which will be better than sending 20-20K to a full-range (yes, they have internal crossovers built-in, but it's not quite the same.)
So how do we hook up 4 (assuming 2 tweets, 2 mid-bass) speakers to 2 front channels? Via an external crossover network, usually (these days) on a PCB (one per LH/ RH channel). You run the outputs from the HU to those crossover boards, then to the speakers from the connections on the PCBs, and they split the frequencies to go where they should.
Downsides to components (I'm sure there are more, but I'll list two...)
- They generally require more power to sound their best (so you should budget for an amp)
- If not properly placed, the discerning ear can 'localize' the sound from each.
Re: the Polks, specifically...
This would be a cost-effective solution, if you decide to skip the amp, and go with a simpler solution. They can be run with an amp, too, if you like. You'd want to run new wiring from the HU to the doors. The Bose amp has the crossover built into it, so if you retain that amp, things get dicey with regard to frequencies sent per wire, ohm load, etc. Another reason to ditch it, IMO.
BTW, I didn't view the link from the TBSS forum that discusses this scenario (?), but will do so now.
(on edit - now that I've viewed it, it discusses retaining / using factory wiring left over from removing the amp. This *can* work, but if you're 'going component', remember that you'll have to plan for your crossover network (since none will be present after the Bose amp goes bye-bye)
Since you have the 'oddball' '02 (IIRC), just make sure the wire colors correspond - I'm pretty sure they were changed at least once during the model run.
Finally, I'll add...re: harness. I love using them, and if you want chimes, OnStar, etc. - these fill the bill. I like Metra, myself (no trouble in either the Voy or Sierra); others like the PAC harness, and I think Crutchfield even sells a 3rd vendor now (although I'd look someplace else for it, cheaper)