I used to think that Cougie, but i punctured after 95 miles at Outlaw this year. I was stupidly cold when it went pssssst, but standing at the side of the road, changing the tube in the pouring rain and ALL bodyheat that i had left in me, went up in steam. I said a few choice words, but i also said never again to tubes. I once punctured at mile 123 of a 125 mile sportive, going fast downhill, when i was stupidy tired. On both occasions i was on GP4000s!!
I use tubeless tyres. So far, so good. Schwalbe One 25c on Shimano Ultegra 6800 wheels. Used a tyre lever to help in puting them on, as nothing to pinch, but was no more hassle and took no more time than standard clinchers. I wouldn't let the installation stories of not being able to fit put you off. If i ever do flat and can't get the tyre off the rim by the side of the road, i may change my mind. I was taken out of the race at Outlaw this year by a flat, so for me, tubes can do one.
I have swum in rough seas and find the most important thing to do is relax. Don't fight the conditions, be patient with your stroke to stay balanced. Let the water take you, if you are taken up on the top of a wave at the point you begin the pull phaze, you may have to pause a fraction longer to keep your balance.
Re pieces of energy bar in bento box sticking together etc. I roll mine in plain flour and then brush off the excess. Takes 95% of the stickiness away. I do the same with ShotBloks as well.
Back to your original question, i reckon you've gone out too hard on the bike as well. Also remember, you went out faster than the pace you had trained at, AFTER a decent length swim, your reserves will have been depleted by the swim.