First, I ride a recumbent, so my experiences will be a little different from yours. This is my aero setup:
The wheels make a big difference, surprisingly so. For any event where I am concerned about time I will use this setup. On the front is a Spinergy Rev-X, and on the rear is a wheel cover over a regular wheel that has a Powertap hub.
With the Spinergy, either it is working correctly or it is broken. None of this "I wonder if I can ride with this busted spoke until I get to a place where I can fix it." Running a wheel cover on the rear gives me all of the durability of a normal spoked wheel. At worst, I'd have to take the cover off to fix a spoke. Time consuming, but unlikely.
No comfort is lost with this setup. The Spinergy rides about the same as my normal wheel.
This setup adds weight. If I am doing a ride with a lot of climbing I may use another setup. One option is to use the wheel cover and a normal front. I still get a lot of benefit from the wheel cover. Plus, it really is a PITA to take it off and on.
For me, always clinchers. Besides the normal spare tubes, I also carry two patch kits, tire boots, and a spare tire. I'd have to have a really bad day for this not to be enough.
In January I did a 200k with another recumbent on a similar bike. He had Zipp 404s with a wheel cover on the back, whereas I was running only normal wheels (Mavic CXP-21 rims, 28 spokes, 2x in the rear and radial in the front). On the flats I was using 240-250 watts to draft him while he was putting out 200 watts. After 5 hours of running at an average of 246 watts I finally had to let him go, and finished about 15 minutes behind him (he was the first finisher of about 75 people, and I was third).
At the 300k, I was running my aero setup, he was running the same thing, and my watts were much closer. I'll never match his efficiency simply because I am 6" taller and 30 lbs heavier. I was the first in (he turned back at the 75 mile mark, leaving me solo for the rest of the event), with the next person 1.5 hours behind.
I used my aero setup for the Death Valley Double on March 1st. Huge mistake. The cross winds made my bike very unstable, at times almost uncontrollable. I'd have done better with a regular front wheel and the wheel cover. By the time I was finished I was exhausted simply from battling the bike.
In mid-March I did a 400k in Arizona. Running the wheel cover and a regular front was a good choice. It was windy, and the Spinergy would have been problematic.
This coming weekend is the Davis 24. The wheel cover will be on for the entire event. For the 150 mile, 8000 feet of climbing day loop, I haven't decided between the Spinergy and a regular front. On the night loops I will definitely run the Spinergy because I can change it out if the cross winds are too bad.
The weekend after is a 400k. I will be running the full aero setup, trying for the fastest time.
How your experience might be different from mine:
Simply put, your sensitivity to the center of pressure (CoP) moving is going to be different from mine because of how far back on the bike I sit. The farther back the CoP, the better. The wheel cover helps this, the Spinergy hurts. You on 404s may have handling problems in cross winds.
Look at some of the newer wheels, e.g. Williams or Flashpoint (sp?). Think about whether you can repair a broken spoke on the side of the road. I can't with the Spinergy, but I could if I had a 303 or 404.
Aero bars work, but how long can you stay in them? Some people can stay in them for hours. But what about the rest of the event? On a road bike I can't use them at all, but that's just me.
Aerospokes work, but I hear they are heavy. Maybe something like a Hed 3 would be lighter.