MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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It is a complex project to tackle first. For removing the raft a small wire cutter is very helpful, not only cutting, also using its lever action. Tweezers are helpful for small bits. Usually I am able to remove a lot of my rafts and support by hand though. Acetone would make your raft weak but also your model so you could drag out a bit of the surface of the model while getting the raft off. For cleanup you can do sanding to get rough surfaces more even. Dremmel should work too but might be a bit too much. Painting acetone on it can then make it very smooth. You could also use acetone vapor smoothing which works very well to make prints overall smooth but for this model it is a bad idea since it will also smooth out and slightly distort the connections.