Yes, I have a PDF opened in Preview. I did not find the plist file you mentioned. However, there were these, which I deleted after quitting Preview. Launching the app returned them.
com.apple.Preview.LSSharedFileList.plist
com.apple.Preview.SandboxedPersistentURLs.LSSharedFileList.plist
After relaunching Preview, I still do not have a "select tool" icon.
Thanks for your assistance. I guess I'll just continue to use PDFPen.