My advise would be to go as slowly as you can bear. I'm assuming this will be the first system you'll have scratch built yourself. Have a look at Russells thread on building a pc as there is alot of good advise in there.

As regards with what to buy, research research research. Plan out exactly what you want and why. Altho you have a very nice budget with $5500 it would be very easy to buy overprice or gimmicky parts.

My reccomendations for what there worth.
1/ Either good P4 Northwood as the newer P4 Prescott will let you get a nice price on the slightly older but still very good P4 Northwood.
OR
AMD64 FX, or dual Opteron system. The FX's will give you loads of power in a single chip, but we'd all love some dual processor power. Plus when Windows, i'm assuming your gona use windows, comes out as a final stable 64bit platform and hopefully soon after a 64bit Maya you'll have a further boost in performance for no additional financial outlay.
2/ Memory. Lots of it and make it snappy. High quality ram pay's for itself in terms of performance. So pay a bit more for Corsair or OcZ memory and you won't regret it.
3/ Hard drives. SATA RAID. SATA so its cheap, and raid so its oh so very fast. If you really want the best get a dedicated raid card as well so you can get some striping with parity checking. Speed and data protection all in.
4/ Graphics. If your serious get a pro level card. The benifits speak for themselves.
5/ Dual monitors. The extra workspace you get streamlines your work flow dramatically. Don't dismiss CRT monitors straight away. You can get some very good monitors at cheap prices now because of there fall from favour.
6/ Cooling. Whatever you buy its gona pump out a serious amount of heat. Don't scrimp on the cooling system. Look into all your options. Watercooling may seem total crazy but with a little bit of common sence you can get a very efficciant cooling rig. The comercail water systems have come on in leaps and bounds in recent years and its oh so quiet.

Well think that quiet enought from me just now, if I think of aything earth shatteringly important i'll post back . And good luck with your rig.