Do not panic, keep calm. I experinced the same situation: My application (140/485 2005/9/27) was rejected on 02/18/2007, and my visa was expired on 04/07/2007. I spend a month in a new application as well as an O1 visa. Both were submitted 03/30/2007. Within a week, both 140 and O-1 were approved. My 485 was approved week ago. You may inquire with lawyers. Chen Dan Hong Law Office may help, really.
I think, it is almost impossible to get success for both MTR and Appeal. As for MTR, you must have some very important supporting documents you forgot to submit. As for appeal, you must know the immigration officer made an obvious mistakes in judging your case, even though, it takes more than one year.
You already have some backup materials (copy of letter). Certainly you have new materials such as new papers, new citations. Preparation a new application is relatively easy. If you have good awards, you reviewed some papers or some important review papers cited your works, you may try EB1. Searching my posters over here, I suggested several people. Hope it helps. Remenber, DO NOT PANIC!