I would second what Cam said. If the hub and rim are correctly matched (ie rim drilled at the correct angle) then it really is quite simple. I have only done one wheel, but had no particular difficulty getting it as right as the shoddily welded Borrani rim would allow. I did it in the swingarm of the bike with a pointer g-clamped to the swingarm to indicate runout. Not rocket surgery.
I do have a machining background, so a bit of experience clocking up 4-jaw chucks helped, but really it is just a matter of a bit of empathy on the tension of the spokes and a methodical approach to chasing the runout.
On the other hand, a friend just got Lightfoot Engineering in Melbourne to change the rim on the front wheel of his SF2. Cost about $500 all up, but most of it was the new spokes and nipples. Labour charges for refinishing the rim and hub, and for lacing the whole thing up were pretty minor. So it may well not be worth your while to do it yourself anyhow, assuming (and that's a big assumption) there is someone you know who will do the job to a high standard. My experience with Lightfoot is excellent, only problem being sometimes long turnaround times and you have to allow an hour if you call him (the two might be related). Top bloke and top quality work in my experience.
If the rim is undrilled, or drilled at an angle not suited to the hub you're employing, or you have some weird offset to accomodate, then you might benefit from someone with a bit of experience to look at the wheel for you.
Cheers
Steve