My suggestion: swap & seal water pumps. Diagnose/tear apart and inspect the head gasket. Both are cheap.
If those don't fix it, here's a useful link:
http://www.rcramer.com/bikes/ex250/rebuild_notes.html
A complete rebuild is both more time consuming and expensive than you can wrap your head around if you have to ask, no offense. I did a bunch of work on mine and it was entirely too much effort for what it was. Then I swapped a built newgen engine in. Besides a few small details, that was very easy.