LimeWire actually does do your point number 1. for most Incomplete files. I believe that the Class that actually generates the downloads.dat is called the IncompleteFileManager.

There was a big version 2.3 fix that keeps active file information more fresh in the downloads.dat file so that downloads will kick in and resume downloading most of the time. You should check out the new 2.3 version for this and try it out.

Thanks
-greg