2003 Or 1998...help!!!

I'd base my decision on what its like under the skin...shock linkage bearings and other various bearings which would give me a general feel for how well maintained it was. I'd pull the pipe and look at the piston skirt, rings, head and top of piston, KIPS, etc., to get a feel of how much money I have to put into it to bring it up to my standards. I'd also consider what mods the two bikes already have that I'd spend money on anyway. I bought a '95 last summer that was meticulously cared for and would buy it again over a much newer one that wasn't as well taken care of. If you own it for several years I would think that condition would come more and more into play as they both get older as determining resale value. Do your home work on them and the answer will become clear to you. Don't necessarily make a snap decision...that's how I usually get burned.

You might also want to consider the DMV and taxes you will be paying for swapping the bikes. Maybe your state doesn't do that, but California will sure want you to donate to Arnold.
For $900 you could have that older bike more tricked out than any '03 out there.
If you plan on dumping it in 3 years, keep the old one and sell it for what you paid for it. It won't decrease much more in 3 years.
BTW if you are in California, the '03 will not have a green sticker! That costs plenty in resale.