You delete the entire folder called .limewire (after you re-open LW it will create a new preferences folder!)
It is normal for files to be queued after you open LW. You need to give LW time to settle down. How long this takes depends on how many incomplete & shared files you have. Files will try to connect one by one, but you need to give it time. Manual searching for sources helps to find new sources after LW has settled down. And don't use the Resume button on too many files otherwise your files will be queued for much, much longer periods.
Here's some hints:
A well set-up LW can start to automatically continue its dwnlding after it's settled down perhaps 2 out of 3 times you open LW. Optimising LW & Maximising Uplds & Dwnlds A (1st post only) & also Part B which is even better & last & least are search & dwnld hints. The latter one I've been thinking about re-writing for some time. That's just for playing it safe. eg- I show all speeds & qualities.