So its been getting cold here the last few weeks, one morning a few weeks back i noticed that my manual trans wouldn't move out of gear, it was frozen. in the after noon it warmed up enough to thaw itself and i changed the oil immediately, it had a but of water in it.. i let it drain for about 2 hours to make sure everything was out. i filled it back up again. a few days later with more cold weather i noticed it was stuck again. and again in the after noon it thawed itself so i drained the oil again and there was still a little bit of water in it. not much at all but i guess enough to keep freeze it. so i did the same thing again. now last night it was down to about -6 and this morning it was frozen again. and its still at -2 so its not thawing itself. is there a good way to remove all the water from the transmission. its been drained 2 times but still freezing. also would it be ok to pour some gas line antifreeze in there to thaw it out or can i run it with just the gas line anti freeze in it until i can get to a warm garage to let it dry out?  its a 96 side kick 1.6L

I would wire up a 100w light bulb like a drop light to the bottom of it and make sure that the breather is open or not clogged up, that would warm it up and get rid of most of the water.

My suggestion....
Once it thaws out again, I would drain all the oil and fill it with diesel fuel and run it through the gears to slosh it around in there (don't drive it very far...just up and down the driveway would probably be far enough).  Then drain the diesel out and do it again.  A couple of flushes with diesel should get all the water out.  Then refill with gear oil.
I've used that method with tcases that I got water in.  Worked great.

Just a suggestion - take the shifter boots off and look through the hole - there should be three boots, the #3 boot attaches to the console, the #2 boot attaches to the transmission tunnel and the #1 boot to the transmission itself - make sure all of the boots are in place and in good condition.

I suspect the #1 boot may be missing or torn - if it is you may have water & muck down in the shifter extension and that will freeze and cause the problem you're describing.

The #1 boot is only supplied with the shift lever (at an exorbitant price) so if you need one try cutting a steering rack boot down to fit.

Agreed, it's likely the shifter that is freezing. Check the boot as fordem said & also the breather to make sure water can't get in. You could use WD40 on the shift forks... use LOTS then sop it up with shop rags & spray a light amount back on to keep the water off.

The number 1 boot is ripped, there a huge chunk missing out of it. Now my next question is how do i clean in there up? With the wd40 or is there something else?

My father had a similar issue almost every winter, being a common sense challenged college grad he insisted on parking his truck in his garage, it has a blacktop floor and is unheated. He would pull the truck in the garage and close up the garage tighter than a drum, then condensation would form on and inside every component

In my case, I didn't have a moisture/freeze issue (I'm in a year round, warm climate), so I had dried, crumbled rubber from the boot and that sort of stuff - so I used a brush & a rag and then added lithium grease - I don't know if that will work for you though.

Mine was also the transfer shifter.