1) I assume you're talking about an amp kit for your sub(s)? I think they're just wanting to sell you some extra stuff. No reason you shouldn't be able to re-use it after only 10 months.
2)'95 XLE system has the amp under the front passenger seat. When you put an aftermarket HU in, you bypass that amp. Fortunately, Toyota put an extra set of wiring harnesses in just for that purpose. Those harnesses are tucked away in the dash behind the stock stereo. Disconnect the harness from the factory HU and tuck it away, then find the two "hidden" harnesses to plug into the new HU. Get adapter harnesses like you would get from Crutchfield or Best Buy, etc., to connect the new HU to the factory harnesses so you don't have to cut the factory harnesses.
This link should help you with the connectors...
http://installdr.com/InstallDocs/Toyota/PDF/869013.pdf
3) Yes, you can put aftermarket 6X9s in the rear deck. The factory 6X9s have a unique mounting pattern though, so you'll need to buy or fabricate some adapter templates to have aftemarket 6X9s fit. I bought adapters like these from eBay...
http://cgi.ebay.com/ebaymotors/6x9-R...spagenameZWDVW
With the door speakers, there's a single cone full range speaker in the lower door, and a tweeter in the door handle. They didn't wire it like a component system though, they just wired the tweeter in line with the full range with a high pass line filter before the tweeter. If you want to use the factory wiring and the amp from your HU, you can just put a pair of coax in the lower door and a new pair of tweeters in the door handles. If you want to put in a component system, you'll have to use an external amp (HU amp lacks power) and you'll need rewire.