Jake,
The options for restarting are fairly drastic.
One is to drain the pond which can be accomplished by pumps, siphon systems, or digging a trench to allow all the water to drain. In this approach, all the water, not just most of it, will have to be removed. I have drained two ponds by the trenching method, one with a trench through the spillway and the other through the dam itself. Both are quick, effective, and won't bankrupt you.
Another option is chemical, with rotenone (sp?) generally the chemical of choice. I've never used it, so will defer to others on its use.
Restarting is a last resort. Be sure of your objectives for your pond before taking that step, i.e. what exactly do you want from your pond? There are many ways to minimize the effects of "undesirable" fish, short of restarting completely. There are several folks on this Forum who can suggest those ways, folks who have had the same fish and same concerns.
My advice:
1)thoroughly consider your objectives
2)review all possible options to achieve them short of restarting and
3) if you are still convinced that restarting is the only way to achieve your objectives, then you've done all you can do to insure the best decision and can comfortably proceed.