I have a 04 Tracker Targa and last night while fishing the aerator decided it didn't want to turn off. I have never had any problems before now. All the connections that I can find seem OK, the switch for the lights is the same so I carefully changed the wires and it did the same thing. What am I missing????

If changing the switch didn't work you may have a relay that is stuck in the on position. Your switch energizes the relay to complete the connection. turning the aerator on and off. Have you tried disconnecting the aerator wires at the switch does the aerator still run, if it does it's probably a relay.  If there are no relays you have a direct short somewhere in the wiring harness where a hot lead and your aerator lead touch in that case you will have to check your harness for worn spots.

What would a relay look like and where would I find it?

This is what my pump looks like............... http://www.cabelas.com/product/Boat...s-Aerators|/pc/104794380/c/104743980/sc/104434380/Johnson-Pump-Replacement-Motor-Cartridges/737729.uts?destination=%2Fcatalog%2Fbrowse%2Fboating-livewells-bilge-pumps-hatches-livewells-aerators%2F_%2FN-1100640%2FNs-CATEGORY_SEQ_104434380%3FWTz_l%3DSBC%253BMMcat104794380%253Bcat104743980&WTz_l=SBC%3BMMcat104794380%3Bcat104743980%3Bcat104434380

Is it possible the pump is going bad?

I doubt it is the pump going bad. When a motor goes bad it shuts off or blows a fuse or breaker. You either have a short to battery + or a stuck relay. A relay is a small box with 3 or 4 wires hooked to it. It can be located anywhere in the wiring between the switch and the pump but will usually be found near the pump. It may be in a relay center with other relays and perhaps fuses/circuit breakers. Follow the wires from the pump back towards the switch. A bad connection would cause a no-run.

I cant find any relays in the system, but i do have an automatic timer for the pump. If I disconnect the timer it still runs continously but the light goes out in the off position. Could this be the cause of my trouble?

If the pump continues to run with the timer disconnected, that is not the problem. If you can access a wiring diagram for your boat, that may provide some help. If not, all you can do is follow the wires from the pump to where ever they end up and see if the power lead is shorted to battery power.

I guess I get the "Homer Simpson Award". After tearing apart half of the boat and not finding anything wrong a friend of mine solved the problem for me with out ever seeing the boat. He asked one simple question.......... Does the boat have an aerator switch up in the front of the boat? You guessed it the front switch was in the manual position. Boy do I feel stupid, oh well it's not the first time and I'm guessing it won't be the last time I do something stupid. Thanks for all the help. I did actually learn a lot about how my live well system works.

"DOH"  Knowledge comes from experience, and (especially in my case) experience sometimes comes from stupidity. lol