Take a look atMake a split library portable. Since things are broken now you might as well put them in the standard layout before trying to fix them.
I would move the library files to C:\iTunes, then move the iTunes Music folder inside that and rename it as C:\iTunes\iTunes Media.Shift-start-iTunes and use the choose option to connect to the C:\iTunes\iTunes Library.itl, then under Edit > Preferences > Advanced click the reset button which should set the media folder to C:\iTunes\iTunes Media. Don't consolidate if prompted. Close iTunes and reopen. You may well find that iTunes can now see the content. If not select a track, press Ctrl+I to Get Info. then locate the lost track. Hopefully iTunes will offer to scan for the other lost files and reconnect to them. If not try my script.
tt2