I did a one at a time parts swap that I got from a local pick n pull junkyard, if your really relying on this car you may want to shell out the extra cash for a rebuilt 5 speed to be sure of what your getting, though my 180k mile junkyard tranny hasn't given me any trouble......yet........
Shifter bolts right in where your auto shifter did no biggie there, cables were the only PITA of the whole project because you have to remove so much stuff to both pull the auto shift cable and install the new manual shift cables. It was mainly just time consuming.
Clutch pedal assembly and clutch master cylinder are the only things that you need to do any drilling. If you look next to your brake master cylinder/booster you should be able to see on your firewall where your clutch master will sit, it's a bump on the firewall shaped like the backside of your clutch cylinder. You'll need to drill three holes there in your firewall , one large enough too allow your push rod and the rubber nub end of your cylinder to fit through and bolt holes to attach the clutch master to the clutch pedal assembly. I recommend making a cardboard template of the backside of your clutch master and inking your holes on the firewall so as to make sure you like the way your pedal assembly sits. You kinda only get one chance to get those holes right....
As for the brake pedal it's up to you, I am still rocking the fatty auto pedal and have only accidentally hit the brake and clutch at the same time maybe 3 or 4 times in four months.
Yep you can use the same axles but take it from me you might as well replace them while your down there if you have the cash, I didn't replace either one because I had recently had one replaced when I paid to have my THIRD auto installed (a painful story) and couldn't remember which one had been replaced and now the driver side is starting to click on me
Oh and the ecu thing, don't believe the hype about having to change it, it makes no difference I can tell you from personal experience. When my swap was done I had a slightly high idle and thought that maybe the auto ecu ran a touch higher rpm. I got so sick of getting mixed info online that I went and pulled an ecu from my exact car at the junkyard (except it was a 5 speed) and drove it around for a week and noticed no difference. Then replaced a vacuum line or two and my idle came down to normal. To be sure I then put back the auto ecu and presto! same results I had with the manual ecu !
Any way if you get your parts all together and a buddy to help you, you could do it in a weekend if you had to......