I've got good news and bad news, folks. First, the bad news.
A phone call to RTA's customer information center reported a 3-3.5 week estimate for when Google Transit data will once again be available to RTA customers. It's already been around three weeks. In the intervening time I've managed to get myself stranded downtown by looking at the wrong timetable. (Rookie mistake, I know.) It's amazing how quickly you get used to using Google, and I want it back.
Next, the good news. Amtrak's Pacific Surfliner trains are now part of Google Transit. Yes, that's right, you can plan your trip to San Diego or San Luis Obispo all from one, convenient interface. Note that the Coast Starlight, Southwest Chief, Texas Eagle/Sunset Limited and San Joaquin Thruway services are not available, so Google Transit may miss some rail options, but still... it's a start. (Note: The San Joaquin trains are available in Google Transit as well. The San Joaquin Thruway bus service, which serves Riverside as well as the rest of Southern California, is not.)
Connecting agencies along the Surfliner route that support Google Transit include SLO Transit, Metro, OCTA and San Diego MTS.