I drained everything and realized the majority of the water came from the bottom of the water pump. I rigged up a hose and funnel and connected it to the back flush port which is teed in to my impeller line. After the second gallon I noticed a bunch in the bilge, DOH! forgot to connect the line to the sea pump after draining.
Oh well off to the store for more!. I pulled the gas tank to clean it this year so I figured i'd remove the carb and drain the fuel system to avoid bad fuel sitting in it., all except the pump.
Is there an easy way to drain that? (stock merc pump) should I put the fuel separator back on?

That's what I call doing it the hard way. Hook up a line to that "T" thingy, fire the engine and idle it till anti freeze solution comes out of the exhaust for about 30 seconds and shut it off. Then if you feel the need, drain it. Anti freeze is also a lubricant and without actually running the engine you cant be sure that it filled everywhere. Was your fuel tank full of crud? Why clean it. Filter and sep not doing it's job? Again, by leaving metal dry over an extended period of time your making it susceptible to corrosion. Add some stable to it, I keep my tanks at about 1/2 over the winter storage. In spring I fill them always premium, change the fuel sep fire them on the old plugs to burn off the fogging agent then install new plugs. After a tank full or 2 no more last years fuel. Just my 2 cents worth tho.

You should always fill your tanks. Less chance for phase separation. Your leaving room for condensation to form. Just don't completely top it off. You'll regret it on that first hot spring day when the expanded gas comes out the breather.

Heated Garage is easier.

I live inland and temp changes are not that drastic, and humidity is not bad either during layup. I always use non-ethanol gas so there is no chance of phase separation over the layup. When I did use ethanol blends I would put stabil in the tank prior to last run of the season. Don't fog engines do to less then six months layup. For carb engines, after changing the oil would just shut it off. Gas will evaporate after a couple, three weeks with much any kind of warmth.

Don't use antifreeze in engines because the main reason is air doesn't freeze, you also don't know if you have 100 percent everywhere. We had a colder winter last season and on iboats we had more folks with cracked blocks then I could count. Almost everyone of them used antifreeze (pink RV) in the engine. Run the engine then drain everything, I only pour the antifreeze into the top of the large radiator hose and power steering cooler just to flush out any little bit of water left there. This to is drained.

Hope you have an uneventful startup in the spring

Your lucky to still have non ethanol fuels available. Wisconsin / Milwaukee, lake Michigan marina's all have ethanol only. Though ethanol isn't all bad. It's a great cleaner. Phase separation normally effects warmer climates anyways. The fluctuations between freezing and thawing with rain or fog and you have a perfect recipe for octane hell in your tank. If you read the fine print on Stabil for ethanol fuel, you'll come away with the realization It's not a guarantee either .

Ya, having lived in NE IL all my life, I'd have to respectfully disagree on most of the above. Draining the block, exhaust, etc of water and refilliing with -50 RV antifreeze will never ever result in a cracked block. No way, no how- The only caveat I've ever seen is 4.3 GM V-6 engines tend to crack in the valley even with minimal water accumulation (ie leaky cover or holes in your shrink wrap).

Evaporated fuel, even non ethanol stuff, leaves behind a lot of nasty crap- don't trust any of it. Fogging oils on true EFI systems pretty useless. Sea Foam and other additvies will help carb'd engines.