When you have all your Run items the way you like, go to HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\RunMRU and export to a convenient directory. When you save it, give it a suitable name, like RunMRU.reg. Now you have a .reg file you can use to replace your favorite Run list.
Wipe all your recent items: Start menu > properties > Privacy > untick "Store and display recently run programs..." > Apply. Then retick it and Apply. Now double-click on the RunMRU.reg file that you exported and OK the change, and you have your favorite Run list back again.