layover in SJU?

I'm looking each day for flights, and after my initial excitement of flying direct from MIA to EIS, I realize that is not the way to go. We will be flying out of St Louis which is basically the end of a spoke in the airline system these days. What that means is we will need to fly to a hub, like ATL or CLT then get another flight to SJU and a third flight to EIS. I'm still searching but what about taking Southwest into SJU? Then we would have to catch one of the puddle jumpers to EIS of course. It seems easy on the trip down and we would like a few hours to mess around in San Juan or even spend the night there. I understand we would have to clear TSA again in SJU the next morning. My question is on the return trip. I think we could leave EIS around 10:30 but, once we get to SJU how much time would we need to clear customs/imigration, and then check into the next flight on a non-codeshare airline like Southwest? I'm sure someone on this forum has done this. Was it the worst idea ever? Any helpful pointers?
Thanks,
Robert

I spent a few minutes explaining this to my wife. She reminds me that in the past when you arrive in SJU you collect your bags to go thru Customs, immigration and TSA. Then you check them back into your airline. I guess it wouldn't matter which connecting airline you use since they are not transferring your bag.
Thanks,
Robert

Well yes and no. Correct you have to collect your bags and recheck. But are they tagged thru and do you have the boarding passes for your connection. In SJU right outside of customs is a drop of to check your bags thru. I do not know if you can get them tagged to anohter airline there. Have never had to think about it.

If you have to got completely out and go to a checkin counter, then leave a lot more time.

We have done this many times on our return flight thru San Juan. We usually arrive on Air Sunshine. You first go thru Immigration, then go downstairs to claim your bags, then go thru Customs. After that you exit the secure area and check your bags at your airline. Then you go thru TSA check and to your departing gate. I would allow at least 1 1/2 hours to get this all done comfortably after your arrival in San Juan.

Why not fly into St.Thomas, there are many direct flights. We are not opposed to the ferries, kind of nice starting with a cold one on the water. We find flying from Colorado, STT is easier and less expensive.

Thanks Eric and Kmon, those are the things I'm wondering about.
Sail2wind, In the past it has always like you said, cheaper to go to STT.
I've been looking and it is currently less expensive to do 2 separate reservations with the overnight in SJU. I was surprised to find it is nearly the same price to go to STT as it is to EIS.
Thanks,
Robert

I paid attention last time we flew a charter to SJU for a connection. Memory tells me it was 25 min from when we landed to checking in at American. There is a lot of walking at SJU. The ag department baggage scan was quick, used the AA kiosks, but TSA was backed up down the terminal. We have PreCheck and we were in line for 25 min. This was a cruise ship turnover day so the airport was a zoo. On a weekend, I would allow at least two hours min.

We do this all the time - separate tickets Cape air and JetBlue. We allow for 2 hours for the connection both ways. This also gives us a chance to get something to eat. What's also nice with Cape air is that if you get there early, you can often get on an earlier flight.

Our group has done this the past two trips (both ways)and it was really easy. We fly Southwest going down to SJU then this trip we flew Intercaribbean to EIS. We got the SJU-EIS for $99.00 each way. After we landed in SJU we got our bags and headed upstairs to check-in for Southwest. We had TSA precheck and it was really easy. Coming back it was also very easy. A helpful airport employee showed us an elevator after we went through customs and got our bags and it took us right to the check in area.

In Wichita it is very tricky to make the trip in one day for an affordable price. We have always had best luck on Southwest for what we need price wise. There is an extra flight in there that some wouldn't like but we have always made it down there and home on southwest.