MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I'm sorry for your loss. Fortunately there are several aftermarket companies that make aftermarket controller boards for the Replicator, and the cost is not unreasonable (on the order of $150), and as a bonus most of them have fixed the flaws that usually kill a MightyBoard. I haven't had to deal with a replacement myself, but I understand that this is one of the better ones: http://www.flashforge-usa.com/shop/parts-accessories/mightyboard.html
As an added bonus, this one gives you a 2560 processor instead of the original 1280, giving more memory which allows new functions if you use the Sailfish firmware. The replacement is not terribly difficult at all, and is mostly just a wire-for-wire swap. There are lots of folks that will help you on the FlashForge Google Group. Those Rep 1's will last a long time, and with care and a few upgrades can print as well as any new printer on the marker (and better than some). Hmm, I see it's $185; more than I thought. I also don't know about the SD/Display board - it may need replacement and I don't know about the cost or source for that one. The Google Group will help though.
If your board suffered a typical regulator blow-up, this is usually easily identified by physical damage to the large regulator chip that is near the switch and power connector. I would really appreciate it if you could take a look there and confirm that and let me know.