Manually building a connection is covered in detail in the Wiki FAQ.

You don't have to pay two fares as long as your connection is under 4 hours (and otherwise meets the requirements for a merged fare). Depending on pricing, you might want to book the fares separately to earn two RR credits instead of one.

There is no way for SWA to automatically protect you in normal ops because they specifically permit hidden city ticketing. A pax might have no intention of taking the connecting flight.

I don't have much experience with HOU. Here is a terminal map. I don't recall it being all that large, and it doesn't look very large on the map. In any event you ought to be able to request disability assistance for your DH.