GNORSK, I pondered the same question on my 99 EX Sport as you did "rebuild for $2000 or sell out".
Well considering that other than the transmission the truck runs great and that if I sold it as-is with the transmission issue I doubt I'd get more that $1000 for it, I decided to have the transmission rebuilt. I hope to get it back this week.
Ask yourself, how much would you pay for your EX assuming it runs good and has a documented newly rebuilt transmission? I ask that question to myself and decided I'd pay around $4000, so given that the rebuild is around $2000 and without it I'd only get $1000 for it, I figured by rebuilding it vs. selling it I save $1000 over buying another one just like it.
I know this is kind of a twisted way of looking at it, but also think about how much it will cost to replace it with another used vehicle which you have no confirmed history on.
My vote is if you like the EX then fix the transmission. If the engine blows up tomorrow you could at least get $1000 for the rebuilt transmission plus maybe $500 for the truck, so your risk is only $1500.
As for whether to rebuild yourself or have it done? By doing it yourself you could save around $1500, but factor in your time, vehicle down time and the lack of a warranty. Also your decision needs to factor in your abilities. Not all of us have the skills and knowledge of "BrooklynBay". I consider myself a fairly good shade-tree mechanic, but there's a reason they charge $1000 for labor just to rebuild the transmission, because it ain't that easy and there are allot of opportunities to do something wrong only to find them out after you put the transmission back in.
Good luck on your decision,
Blueraven