I've built a MDF CNC router as well but I haven't even moved anything yet (still waiting for my PC from ebay to arrive). My table top is 3/4" MDF and it's 21 x 36 inches. I purchased some t-track from grizzly.com (actually through amazon.com) and got 4 lengths of 3 foot track. It's the typical 3/4" wide and 3/8" deep and they are only about 8 bucks each. You have to drill your own holes and there's no screws but that's alright. Also, rockler.com is having a sale on 4' t-track and it comes with t-bolts and knobs for only 15 bucks. Don't know about sealing MDF though, I think I might paint mine at some point. The way I designed my mill is I built a sturdy (torsion box type) table and then put another layer of MDF over that as a sacrificial surface. If I have to change it at some point I just have to unscrew the t-track and route slots in a new piece and slap it back on top. Hope this helps.
P.S. what endmills are you using. This is an area I'm having a hard time figuring out. I'm using a lamenet trimmer with a 1/4" collet and I was wondering if there is a set of endmills with a 1/4" shank. Maybe an assortment of ball, flat etc.?