No I think that's fine. From memory you can set particular tasks ... not necessarily all tasks at one time. I'm a little wary of using Cocktail, etc. because in some cases it resets permissions in an undesirable manner. At least it did for me & took me a while to set them up in the custom fashion I prefer.

A basic repair permissions is generally all I do using Disk Utility. That's recommended after system updates & also recommended by some people after installing software.

Something else you could do is delete your LW prefs whilst it's closed but that will mean you'll lose all your settings & filter settings including junk record. The LW prefs folder is found here /Users/your_username/Library/Preferences/LimeWire

Other recommendations to reduce system drain are ...
After opening LW wait 5 to 15 mins or longer before using. Let it settle down 1st.
Go to LW's prefs>Speed & tick disable Ultrapeer Cap. & press apply button.
Set both uplds & downlds to autoclear.
Close all LW windows you don't need open at that time.
If you're not in front of your comp, then hide LW in the dock.
Reduce uplds to about 70-80% or more. Reduce downlds to 80 or 90%.
Don't use the Resume button on all incomplete files. This can have side-fx such as affect LW's connection quality. May queue your files for much much longer. This will also stress LW & your comp. If you use Resume/Find sources then just apply it to a couple or so at one time.

Make sure your OSX partition/drive has lots of spare space. All OSX apps including the system use Virtual Memory (VM) which means they store memory temporarily on the HDD. You can monitor this via the Activity Monitor which you'll find in the Utilities folder. I save all my files onto a different partition & my shares are also on different drives. Something else you can try is set up a test account & try running LW from there to see if you have same issues.

BTW the LW you're using has bittorrent support if you're interested.