Converting from wav to acc will have decreased the quality a bit. Whether or not that is significant only you can tell. Hopefully you still have the originals somewhere. If you want to go back to the original quality then you can use a script called ConvertFormat to switch the originals into AppleLossless. It takes care of the housekeeping after each track is converted.
I find iTunes and iDevices work best if all tracks have embedded art. I have two scripts that can help with this; CreateFolderArt and EmbedFolderArt. The scripts have slightly different functions:
CreateFolderArt ensures that every album folder ends up with a Folder.jpg image which is the art that iTunes already knows about. Side effects are that if artwork has been updated in iTunes the folder art should be updated also, and if any track from the album doesn't have embedded artwork it gets embedded.
EmbedFolderArt was actually written for someone who already had various artwork images stored in the album folders and wanted them added to their tracks, but not if iTunes had already downloaded a better quality image. It creates new files of any store art with the name iTunesArt.jpg, then embeds the largest image by area in the album's folder, based on the premise that this is likely to be the best image.
In either case you could search and destroy the images in the folders after they are embedded if you don't want them.
tt2