Finally, finally, I have my livewell situation under control. This has been a frustrating but interesting project! I'll do my best to explain the process:

Materials:
100 qt Igloo cooler with small hatch lid (Sport Mart)
Rule Transom Mount Livewell/Bilge pump - 500gph (Cabelas)
3/4" Cabelas Premium Livwell and Bilge Hose (Cabelas)
Adjustable Livewell Timer (Cabelas)
Attwood Recirq Kit (Bass Pro)
Brass Two Position Toggle Switch (Cabelas)
Wiring for everything, 14ga. I believe
Terminal hardware for the wiring
3/4" Ball Valve (Osh)
3/4" removeable fittings for the water lines (Osh)
2 ton epoxy
Various other glues

Dilemma:
My basic idea was to be able to do the following: Pump fresh water in, Recirculate water, and pump old water out. Sounds simple but it's not as simple as it seems when you're dealing with a jon boat.

The big dilemma is how to get water OUT of the cooler. On a normal boat you drill the outflow hole above the water line but below the lowest level of the livewell. Then you have two drains on the livewell, one at the top and one at the bottom. That way at the end of the day you can drain the entire livewell by gravity using the bottom drain, and during the day the outflow hole at the top causes excess water to drain out.

With a jon boat, the bottom of the livewell is below the water line which means the only way you are getting the water out is with a pump. On my boat, the waterline is almost even with the highest water level of the livewell so even draining excess water out the top of the livewell by gravity would be difficult and not always reliable (say if the drain hole is in the rear of the livewell and two guys stand on the bow and the boat tilts forward).

Solution: After giving up on any kind of gravity based solution to getting water out, I settled on a recirculation pump that would double as a drain mechanism for the livewell.

The overall setup is like this...

Water comes in via the transom mounted bilge pump via 3/4" tubing. This pump is on an on/off switch. The connection to the cooler is via a threaded fitting so it can be detached.

The recirculation pump is mounted on the side of the cooler at it's lowest point. It pumps water from the cooler back into the cooler to aerate and oxygenate the water. This pump is on a timer switch and also has a detachable fitting for the hose. If I need to pump the water out to replace the water (bleeding fish) or empty the livewell I can unscrew the hose and point it over the side. Note that the Attwood recirq pump does NOT have a long enough tube on it to reach through this type of cooler. I was forced to glue the pump in place and glue the screen in place on the other side.

The cooler itself is strapped to the deck with quick release clips. The wiring to the recirculation pump has clips that allow it to be detached also. At the end of the day, I can pump all the water out, detach the whole thing, swish it around in the lake to clean it out and be done.

Improvements: There are two aspects that I am still unhappy with.

1. The transom mounted bilge has two problems. The first is that it will start pumping water on it's own when the boat is going full speed. To solve that I put a ball valve on the hose. The second problem is that the pump catches the water that flows under the boat and causes the boat to steer slightly to that side. Just enough to be annoying when driving. If I could do it again, I'd be braver and go with a through hull fitting.

2. I'd like to have a switch or lever on the recirq pump to switch between recirculation and pumping the water out and over the side of the boat. It's possible using a 3 way joint and two ball valves but I'd like a cleaner solution. Any suggestions are welcome as I haven't seen the right part at the hardware store.

Here's some photos of the whole setup:

recirq line (center of cooler) raw water (right)
http://www.calfishing.com/albums/triton_1546mv/aaj.sized.jpg

inside view (holes are coated in with epoxy to seal foam)
http://www.calfishing.com/albums/triton_1546mv/aan.sized.jpg

screen on recirq pump
http://www.calfishing.com/albums/triton_1546mv/aam.sized.jpg

recirq pump and tie downs (make sure to tie a knot around the tie down straps to keep them from loosening)
http://www.calfishing.com/albums/triton_1546mv/aal.sized.jpg

cheap electrical connectors, good if you forget it's plugged in while lifting it out
http://www.calfishing.com/albums/triton_1546mv/aak.sized.jpg

raw water switch (left) and recirq timer (right)
http://www.calfishing.com/albums/triton_1546mv/aap.sized.jpg

ball valve on raw water line
http://www.calfishing.com/albums/triton_1546mv/aao.sized.jpg

some perspective on the size of the cooler, this is a 13 and a half pound fish
http://www.calfishing.com/albums/triton_1546mv/aaq.jpg