I ended up removing the stock amplifier and bypassing it altogether, though I did use the original wiring for the door speakers. It was essentially a 1-day project (spread over 2 days) upgrading from a Memphis Audio 2-channel amp for a sub to a 4-channel Eclipse and DEI Studio 6.5" components up front.
When I removed the stock amp I cut the connectors off for the wiring to the door speakers and connected those to the crossovers for the component speakers. This way I did not have to run my own wiring to the doors, I just used what was already there. The door speakers came out without issue and the DEI Studio 6.5 fit as close to OEM as you can get (after cutting the outside trim ring on the DEIs and removing the "lip" around the plastic speaker housings for OEM door speakers). I removed the OEM dash speakers, cut templates from cardboard using the old speakers, and currently am using the cardboard templates as mounting plates for my tweeters

(not a long term solution, but I didn't think ahead when starting this project and so I used what I had).
I also used this time, having everything apart, to conceal the microphone for my headunit (Pioneer FH-P800BT). I ran the wire across the dash, up the driver's A-pillar, across the headliner, and replaced the stock phone microphone with the Pioneer mic. I just used a piece of foam weatherstripping to hold the mic in place on the plastic clip/trimpiece. This should keep out noise from the roof and filter back my voice in the cabin.
All in all, I'm fairly pleased with how the install turned out. I still need to play with the amp/crossover settings to dial in the front speakers and sub (also give some time for the components to get "broken in"). The door speakers fit great, dash speakers went in fine, and I was able to find space for the crossovers above the driver's floor panel and behind the glove compartment on the passenger side.
That being said, here are my gripes:
1) It sounds as though the sound imaging is really bad upfront now, with the tweeters in the dash and the 6.5" midrange in the doors. There is too much separation between the high frequencies from the tweeters and the midrange sound. The OEM setup was okay because the 3.5" dash speakers produced a little bit lower frequencies and the door speakers were mainly for mid-bass. I think sound quality would greatly improve with a 3-way setup up front (3.5" or 4" in the upper/front door location in addition to the lower door 6.5" and the dash tweeter). The other option would be kickpods, but unfortunately I have not seen/heard of anyone making these for Saabs.
2) There is not alot of room above the kickpanels for mounting crossovers and such. My Volvo had alot more room and was easier to take apart and put back together.
3) No wonder there is so much road noise that comes in through the front doors, there are holes everywhere! I was going to cover the insides of the front and rear doors with peel & seal but when I got the front door panels off and pulled back the weather foam/insulation, there were large openings with very little metal on which to apply soundproofing material. I was greatly disappointed. I used peel & seal on all the doors in my Volvo and it noticeably reduced incoming road noise.
Wow, that was alot longer than I expected it to be. Anyone else share my concerns with sound/build quality? Any solutions? Ideas?