First, let me offer that "soak everything" to you might mean something completely different. With that in mind, lets march on with the assumption our "soaks" are similar.
Legend has it that WD="Water Displacement" and 40 is the number of times it took them to get it right.
The good: WD40 displaces water (duh) and it happens to be electrically non-conductive - so it wont be shorting anything out. For a dizzy cap full of water that you need to make run fast WD40 sprayed inside will displace the water and allow the cap to fire correctly getting you back on the road. I carry a can with me almost all the time, because I have personally had this happen AND had WD40 fix it! Connectors that have had water forced into them (think: pressure washed) can be opened, sprayed with WD40, given a few minutes to settle, and then put back together without the usual water problems (shorts, false sensor readings, corrosion of the connector, etc).
The bad - WD40 can damage some finishes, and although it is claimed to be a lubricant it also "cleans" - which means it has the potential to dissolve other lubricants from where they might need to be. (Soaked, vs lightly coated, vs drenched repeatedly?) With this in mind, you could have failures down the road. I'm not saying you WILL have failures - just that you could. An example would be a throttle linkage - WD40 strips off the "grease" and now it runs metal><metal because the WD40 is too thin to protect like the grease. As a result the part wears faster and fails prematurely. Same happens with door hinges - WD40 stops the squeak temporarily, but its too thin for the load bearing so the part wears and the trouble comes back. Again, just a possibility from an unlikely example. (I'm tired, please forgive me if I'm not making sense or using stupid examples.)
I do not believe WD40 has the capacity to cause the problem you are describing with the transmission. Changing your fluid/filter is not going to solve the problem unless a) the
trans got water in it, b) the vehicle has some coincidental mechanical failure that involves a plugged filter or contaminated fluid, or c) I'm just way off in left field. Hope I'm in left field.
If it were my ride, Id start by using some engine degreaser to get the WD40 out of there, and then lubricate any moving parts as per the manufacturer.
Some other things to check: Make sure no vacuum lines are cracked/broken, make sure no electrical connectors have water in them (WD40 might help here), make sure nothing is unplugged, and (obviously) make sure the fluid level in the
trans is correct.
If everything seems OK, the next stop might be a transmission shop so they can properly diagnose the problem.
Best of Luck.
Blade