You'd be very lucky/happy to get anything near $2000 in the current environment, I reckon.
As oldyzman said, they're a great bike that everyone loves, but they're also the oldest bike in the Evo class, so they're at a significant disadvantage against the bikes that have full long travel suspension etc.
And I'm going to ride you for fitting the wrong plastics again.... Obviously they're not hard to change, but they're among many details that will turn away the purists from this particular bike.
So really, you're only going to sell the bike to a racer - and if you were in the market for an Evo 125, you'd have to ask yourself whether a YZ125E the most competitive bike that you can buy for $2k....
Which is not to say that its worth nothing - the fresh rebuild means that it should be painless racing for the new buyer, and they ARE a good fun bike to ride. Good, honest, race-ready 125Ds seem to go for around $1000~1500 on Ebay.
I'd say that your E would be in a similar range, maybe a smidge more - the lower inherent value as a race bike being cancelled out by the fresh rebuild.