Good replacement speakers?

If you still have the stock HU, I wouldn't even bother replacing the speakers. The way the Mach is setup is that you have 3 seperate amps for the 8 speakers(4 mids and 4 tweeters). Here's a link that'll give you an idea: http://www.flemworld.com/Mach460/mach.html The two rear ones are for the midwoofers in the doors and the rear deck, and the other one behind the radio is for the tweeters. If you try replacing the mids in the door/rear while still using the stock amps, they'll be low-passed, and you won't get anything higher than the lowpass frequency. This is the main reason why you can't really 'drop' in any replacement speakers with the stock equipment.

If you want to improve the quality of the Mach 460, and I'm not talking about just adding subs, your best bet is to replace it all at once; HU, amps and speakers, so it might be better to save up a little bit for it, and do it all at once. Then just run the new speakers off either the HU, or a seperate amp.

For your other question, the stock size is 6x8/5x7 all the way around. You can fit a 6.5" or 5.25" in the stock positions, but you'll need to either buy an adaptor, or make your own.