Well I've had the speakers (decided to go for Focal speakers in the end) and amp fitted a few weeks now and have slowly been fine tuning them. The clarity over stock speakers is brilliant. At first I was still getting a bit of hiss (although very minimal compared to before), but after I adjusted the tweeter's cut-off frequency it has reduced it more. I decided not to get the underseat sub because I am considering using the rear speakers as subs. I've still to look at how much room is in there though. While I've had the door cards off, I have sorted out a lot of the rattles that were bugging me before, so it's not completely necessary to have separate subs, but I still think it would be good to have it separate from the mids.
Fitting the speakers in the doors was a lot more work than I thought it would be. Originally I just cut the holes bigger and bolted the speakers to the metal skin, but they fouled the windows when opened. So I then cut 12mm MDF rings to space out the speakers, so that they didn't foul the windows. Also put some sticky foam between the 3 materials to seal it all nicely. And I had to dremel out the inner plastic door cards for the speakers to fit through. Managed to get the standard covers clipped back on though, so it's a complete stealth install
The tweeters fitted in to the standard plastic mounts after filling them a little wider.
I put some velcro on the bottom of the amp and it now sits very neatly under the passenger seat, with just a little blue glow from the LED giving it away. I'm really glad I didn't go for a boot install