Some of your issues pertain to "features" of Limewire, can't give any advice there. But for one or two points I found solutions.

If you make a copy of your downloads.dat file from the incomplete folder (save it elsewhere obviously) and replace it after a crash or quit where you have lost your downloads queue, then you will have the downloads queue from the point at which you saved it (worked for me when I was having the same problem, anyway, but kind of a hassle).

All my Limewire crashes in OSX (several times a day, bad and restorable only with a full restart) were addressed, I'm sad to say, by limiting the # of files I shared. I know, it sort of undermines the whole gnutella idea, but Limewire was bogging and crashing to the point of unusability until I cut down my shares from 10,000 to about 1300. From then forward it has worked perfectly, not one crash.