If you can get to it with just the upper manifold off, you'll just need to replace the upper manifold gasket and the throttle body gaskets. IIRC, there are two gaskets for the throttle body, one on each side of the heater plate. I think I would replace both the upper and lower manifold gaskets, just to be on the safe side - it would suck to replace just the upper, then develop an air leak on the lower side in six months... 
Plus I don't think I could get to those heater lines with just the upper off, but it has been a few years, so I may be wrong.
This is an excellent opportunity to replace all the rubber under there, too - the FPR vacuum line, the coolant hoses, and the emissions-related stuff: the hose to the ICV, the hose to the charcoal canister, the short 2" sections of 8mm fuel line that connect the fuel rail to the fuel lines, etc.
The nuts that hold the upper manifold to the lower manifold, and the lower manifold to the head, are those single-use 13mm ones that are supposed to be replaced if you remove them. You should be able to reuse them, though, just add a little Loctite to them when you put them back on. (That's a 13mm socket to remove them, not a 13mm stud they fit on, just to be clear!)
AND, you can also replace the o-rings for the fuel injectors now, as well, since you'll be able to access them with the upper manifold off.
I would (or I should say, I did) have my injectors cleaned and rebuilt by Rich at Cruzin' Performance (http://www.cruzinperformance.com) while I had it all off, in addition to all the other stuff. I hate having to pull something apart more than once if I can replace everything at the same time. Injector servicing ran around $11/ea for the injectors and included new pintles, screens, and o-rings. You're supposed to replace the injector clips when you remove them, but mine were in good shape so I reused them.
I also painted my upper and lower manifold sections while I had them off, since I got tired of looking at cosmoline. POR-15's Marine Clean does a great job of stripping the 15-year old crap off before painting, or you could take them in and have them stripped and powdercoated.
I've attached a few pictures of the work in progress when I did it.
Great writeup, put it in the writeup section. Oh.....is everybody elses manifold nuts 13mm? because mine had a 10mm stud W/ a 11mm nut to hold the manifold on and they look stock. they where coated in cosmline.......one more thing: i dont think you need to take the TB off, i did mine without removeing it but if you do make sure you get the metal TB gaskets. BMW makes paper ones (i think they where for the E36) and they suck, so make sure they are metal. just my 2 cents:)
