My first guess is that the fastest, easiest way to solve the existing problem, and future potential ones as well, is to junk the site. That is, perhaps register another name, copy your existing code over with the name change, and put it back up on the server you're using. Then just delete the old site. Whatever bad links exist now point to some old, no longer existing site, not ou brand new fresh one.
Let me add another point. It seems to me that a brand new site that suddenly has 250 inbound links is going to trigger some concern with the search engines. In the past when I was doing SEO much more intensively then now, I tried for a "slow creep" in the beginning. If I could afford the time I'd get out my old DandD dice and use them to generate random popularity. My plan would be something like:
Register site.
Wait 1D6 days before adding any inbound links.
Add 1D4 links.
Wait another 1D4 days.
Add another 1D4 links.
Wait another 1D4 days.
Add 1D6 links.
Wait 2 days.
Add 1D6+3 links. etc.
I found that the slow creep almost always worked better than the horse pill growth, especially in the beginning.
Of course you mileage and needs may vary and getting 250 links instantly is required. But if it isn't ...