Was working on my 98 Outback and after reconnecting the battery the keyless remote receiver started continuously clicking. I was unable to stop this until I found the remote, locking and unlocking with remote got it to stop. Is there a way to stop this without the remote?

Try cycling the key from off to the full on (not start though) position 10 times, in fairly rapid succession. This is a bypass for not having a remote on some security systems. YMMV

Ha, don't ya love that, did your parking lights blink too? I did the same thing with my 97 OBW and was very confused. There is one way to do it, although I think in the manual they suggest using the remote, but by that box that was clicking, around the hood release, or somewhere in that vacinity should be a button that is the bypass/remote programmer button. Before I got the factory security upgrade mine was zip tied behind the square keyless entry module(clicking box). That button should take care of your problems in the future.

Check your manual. My wife took the OB to the food store, only took the key. Locking the door will set the alarm, it went off and someone that owned a Subaru told her to cycle the key 4 times (check manual) alarm then goes off. This is to prevent someone cutting your battery connection and stealing the car.