I wanted to thank everyone for their advice and post a follow up for anyone else taking this route to Cozumel.
The short version - at 40min layover in Houston heading to Cozumel, especially if landing at concourse B and leaving from concourse E is really tight, and very stressful. Especially if you think you can put a legal sized carryon in the overhead bin of a ExpressJet (not going to happen, costs another 5-10min). And a scheduled 90 minutes to clear customs and make the next plane barely worked for me but I could see this being far too little time if the connecting flight was at a different concourse or there was more heavy international arrivals or the first flight was late. As the other said, allow more time for this type of flight - I would have liked at least 90min layover on the way down maybe a 3hr layover on the way back.
The long version....
On the way down, the scheduled layover was extremely tight. The plane out of MSP was a ExpressJet Embraer 145. My wife (a pilot) warned me that it would push out on time but not take off on time - she was right. We sat about 100ft away from the gate for about 10min before taxi and takeoff - of course that just made me more nervous (layover now 30min). But I think the overall schedule must account for a lot of this as we landed almost exactly on time (layover back 40min). Then the taxi into the gate took quite a while (now 35min layover).
Of course, Fin59 called it. I travel with a L&M Video housing in a pelican 1510. The flight attendant let me try it in the overhead, made it in okay but door wouldn't close. So plane side check of lots of $$$$ of gear. At first no claim ticket, so I said something and the baggage guy was great, came back on the plane with my claim ticket. Anyway, moral to story even though I was first off the plane it took at least 5 minutes to get my pelican case (now only 30 min to make next flight).
So I did the mad dash half walking fast and half running. Took the tram, had to wait about 3 minutes for the tram and another 5 minutes or so before I was in the international concourse . Fate would have it, that Cozumel flight was at the furthest away gate. As I ran up they were waiting for me. I had 3min to spare. I got on, we pushed off and made Cozumel about 10min early.
If I had to guess, I think the concourse B to concourse E walk/run/tram time took me about 25 minutes. Absolutely no time for bathroom, food, etc.
Would I do that layover time again - most likely not. I'd much rather have closer to 90min or more just be safe. My wife told me that since the ExpressJet and main flight were both Continental, they would be more likely to hold the flight. So, doing this same layover with two different airlines might be even riskier.
The baggage (one checked bag) made it through no problem.
The return flight was also tight, even though I had 90min scheduled I ended up with less time than the 40min layover on the way down. We were about 20min late leaving Cozumel but they did a good job of making some of it up. When we landed I only had about 75min to make the next plane. I think it took about 60min to deplane, go through the passport entry, get bags, recheck bags and re-enter through the full security search of carryon's. This final security re-entry took the longest and had the longest lines so don't assume that the passport and baggage re-check are the worst of it. Thankfully there were no big planes arriving at the same time.
Where I got lucky on the way back was that my final leg home was on a regular jet which was also at concourse E so I left expecting the mad dash only to have to walk a short ways. Of course, they had changed the gate assignment so in the dash to get there I went to the wrong one (youch, next time take 1min to read the board). I got to the actual gate (still in concourse E) with about 10min to spare but they hadn't even started boarding yet so it was nice to be able to use the bathroom, get something to drink and then fly home.
This flight was almost $300 cheaper than the rest of my group paid for a non-stop. Was it worth it - yeah I guess but had I missed a flight, it really would have sucked.
Thanks again for all the suggestions and help and I hope this info can help anyone else in a similar situation.