That sounds like a good price; I had my IMS replaced at The Porsche Specialist in Broomhall by Kevin, and the price was $1350. My RMS seal and clutch etc. had been done by the previous owner but he elected not to do the IMS at that time. (It was the first thing I did before even taking delivery of the car)
The transmission service - I did it myself and it took around 45 minutes (but I already had the car jacked up and on stands for other work; add another 30-45 minutes for jacking it up and letting back down, and around another 45 minutes to an hour for taking all the braces and stuff off, but all this will be out of the way already since they are doing the IMS) and I got the Porsche Trans fluid from ECS Tuning, 3 liters at ~$30 a liter (if yours is a tip then you will need much less I believe). So figure on around $90-$100 for the fluid, there are no crush gaskets on the fill or drain plug on the transaxle (at least on 2000S) and since they will be using a lift maybe an hour of labor? so maybe $175 - $200 for the trans oil change?
If you do your own oil changes (and at least with the S there is no funky socket required) you could do the gear oil change yourself and save some $$$
(Edit: I am not sure if you have to take all the bracing and plate off the bottom or you can fit your hands up through it; I had mine off since I was doing other work already; and these plates/braces will already be off when the mechanic does the IMS so maybe that is a good time to go ahead and knock it out)
Pelican Technical Article: Boxster Differential / Manual Boxster Transmission Fluid Change - 986 / 987
2000 Porsche Boxster Roadster S H6 3.2L Drivetrain Manual Transmission - 99991754600 - 75W-90 Gear Oil Manual Transmission Fluid - 1 Liter - ES#1513799
Steve