On the transfer to Railay, I seem to recall when I stayed at Sunrise Tropical, I got the transfer through them. The price was reasonable. Otherwise, when you exit baggage claim, go to the transport counter and be sure to tell them you're going to Railay.

According to their website it's 1200 baht each way (I'm assuming per person).

This is probably a really stupid question but how do you get your originating airline to check your bags through? So I'm flying Cathay Pacific on the inbound. How do I get them to check my bags onto the Thai Airways flight to Krabi, assuming I will take the 1:50 flight? Do I just ask at the counter when I check in?

You just ask. Since it's not on a single ticket they could say no, but they seldom say no.

Yes, show them your onward ticket and ask that they check your bags through to Krabi. Make sure the destination tag on your luggage is fro Krabi. I've never had an airline decline to check my bags all the way through (but of course, I avoid budget airlines).