I'm a decent swimmer. Last year I usually went top 10 or better in my age group. This year I spent even more time improving my swim fitness. I really thought I could swim it in 30 minutes or less. I completely underestimated the cold and chop.
The chop:
I was mentally ready to swim at my threshold. I've done numerous threshold sets with 5 seconds or less recovery. However, those sets were performed in a pool where I could easily breathe every stroke or even every other stroke. What I didn't account for was having to hold my breathe longer, or coming up for air only to get a mouth full of sea water and having to wait a couple more strokes before being able to breathe. The chop was random and relentless, there was no pattern to it that I could time my breathes on. The wind seemed to be blowing in from the west which made breathing on the right side very difficult.

The cold:
I couldn't feel my hands let alone my arms. My feet and face were numb too. This made it difficult to swim at an all out effort. I felt uncoordinated, almost like I haven't been in the water in a long while.

The chop made it very difficult to site. I was alone most of the swim. I saw some swimmers way to the right of me which made me think I was swimming too far left. However, when I look at my garmin route, it seems I swam the most direct route I could have in those conditions. I was completely surprised to see the beach in front of me. I thought I was way off course.

Not swallow so much sea water.
Warm up prior to the swim. I should have brought some bands with me.

Got out of the water and motored up to T0.5
Stripped my wetsuit put my shoes on and headed for T1.

Not put on socks for the bike. I didn't need them. I also didn't need to put on my bike shirt. I really never was cold on the bike.

Had some major GI distress from swallowing too much salt water. I didn't want to eat or drink and I finally forced myself to eat a GU at mile 10 and 14. I also tried to drink some water but just couldn't.

I chose to race with my road bike. I read several reports of crowding on this course and thought it might be a better option for handling. Even though I thought my swim was subpar, it still put me out in front on the bike with very little crowds. I really could have used the TT bike with the nasty headwind coming out of the west. The climbs were steep but not very long. I think a TT bike would have been fine and might have shaved off some time.

I forgot my bib and had to turn around to get it. Lost about 20-30 seconds

Not forget my bib

This is where the wheels fell off. I had some major stomach cramps going on. Not your ordinary side stitch. These were major to the point where I couldn't run without bending over in pain. I knew I was going to have to run the first two miles at 7:00 - 7:30 pace and the best I could do was an 8:30 pace. It was like I had a speed governor built in. anytime I tried to push it, my stomach would prevent me from doing so. My legs felt great though. I also had too pee really bad. I kept looking for a place to go but there was none. I finally stopped by the side of the trail. It felt like an eternity. Probably lost around 60 seconds here.

I didn't start to feel better until I hit the sand ladder (2:55). By this time my avg pace for the course was a whopping 9:50 min/mile. I knew I had a lot work to do. My stomach started to feel a little better and I could push it a little more.

Pee in the wetsuit. I had to go when I was on the boat but somehow forgot when I hit the water.

Stomach issues

After a week of trying to figure out my stomach issues I think I've figured it out. I think it might have been due to all the sighting I had to do due to the choppy water. This put a lot of stress on my core. I noticed this after a hard swim I did a week later. I tried to simulate the Alcatraz swim by holding my breath a bit and sighting a lot, I got out of the pool and my stomach just hurt. So a combination of not exhaling (causing me to swallow air) and frequent sighting.