Every time it rains (which is starting to be a daily occurrence around here), my truck acts like it has a dead battery. I can jump it fine, and it will run without any issues.

Here is all the information I can give you about the problem.
2000 DII
When I crank it, it cranks like battery is dead.
It will go click click click like battery is dead.
The alarm goes off when I stop trying to crank it (I believe because it doesn't remember me inserting the key, because the battery went dead, I could be wrong though).

It ONLY happens when it rains. When it's dry, no issues at all.

 

And, you have never recharged the battery from when it first died.
Just driving it around town will not recharge a battery, especially when they are old.
Drive down to your local auto parts store and have them check the battery/alternator and youi'l probably find it is time for a new battery

 

I have charged it, a few different times. I have a plug in charger, fully charged on auto.

Battery is less than a year old

I'd be willing to try the new battery thing, but I don't drive it around town, I commute to work about 77 miles one way at the moment, so when I run it, it runs at highway speeds for a decent distance.

The issue is that, I know it is probably hard to believe, is that it only happens when it rains outside. When it's dry out, no problems. When it rains, instant dead battery. Being as I am staying at my parents house while I finish up a college degree, my father didn't believe me until he started to pay attention. Seriously only happens when it rains outside. I'm thinking the humidity in the air is causing a faulty connection somewhere/arcing which is draining the battery.

 

You have corrosion on the inside of the terminal or where the cable joints are, most likely.
It may not look like much but take it apart and clean the connections.

 

You need to go get it checked as already mentioned and let us know what you find.

 

The next time it does it dont jump start it, check the battery voltage with a voltmeter and see if the battery is actually dead or not.

 

Will do, I have a volt meter. Most likely tonight, as it looks like it is going to rain

 

Once it starts to rain and has been raining for a hour or so go outside and walk all around the truck and listen for any noises, any clicking, electric motor running, etc.
Dont open the doors, dont use your remote, leave it alone so that all is quiet and she does not know what you are doing.