Congrats! Im in the same boat actually. Down from just over 300 pounds to 250 as of Sunday. Ill be going into a sherrif's academy either this August, or Jan '09 depending on A - my preparedness (sp?) and B - if my connections can get me into the August academy (though it might be to late).
Until recently I havent ran since high school, need to get my time up to a 14 minute mile and a half. Not to mention all the running during training days.
Ive been following Starting Strength with the beggining runners program from runnersworld.com. Had to repeat the 'first week', 1-minute running (7.5 mph), 2-minutes walking (3 mph), for 4 weeks to work on form more than anything else, and no longer any expierence any ankle or knee pain. The program is an 8-week progression to a solid, 30-minute run. You might want to look into it.
Other than that, cant really offer much help, just tell ya what Im trying, though I still have some distance to go and am far from being an expert.
But again, congrats, I can tell ya from expierence, its a long, hard road, but your doing a damn good job.