This paragraph is a revision to what you read below. I would do the patch first and then use the WD-40 afterward. I just recalled that the hole was real easy to find after doing the WD-40 because there was a ring of oil surrounding the hole, which makes me wonder a bit whether I will end up with a good seal on mine. If you do the patch first, you won't get the WD-40 coming out of that hole to cause a potential problem.
From reading through the thread on hdforums.com, it doesn't look as though anyone is getting anywhere with the MOCO for a fix from them. In case anyone hasn't been following along elsewhere, water is getting into the swingarm through a small hole in the front of the swingarm and then draining out of a hold that is covered by the belt guard cover. If you are having the problem, you may see rust colored dirt on your belt guard cover. I believe this only pertains to 09 Touring models. Follow along here and I should answer all the questions that are popping up in your head.
If you patch the hole in the front of the swingarm so no water can get in, then there's no reason to do anything to the drain hole at the belt guard cover. Here's what I did on mine: First I removed the belt guard cover, cleaned up the area, and sprayed a whole heck of a lot of WD-40 into the drain hole. I let the WD-40 drain back out and I got quite a puddle on my garage floor, so remember to put something under there before you start spraying. I left it sit for half an hour or so and then wiped off any excess at the drain hole. By the way, the drain hole is covered by the belt guard cover and less than an inch to the front of the center bolt on the belt guard cover. Then I reinstalled the belt guard cover. Operation complete on the bottom part. Note: Don't remove the front bolt on the belt guard cover. You only need to loosen it and slide the cover forward to allow the bolt head to pull through the larger opening in that slide hole.
Now, to deal with the hole that needs patched in the swingarm, first you need to locate the hole. Grab a flashlight! In the first photo, you will see a hose behind your oil cap (in the photo it has letters and numbers on it starting with Y-HHS 300). If you look down through the opening just to the right of the 2nd zero in "300" on that hose (between that hose and the larger wrapped wires just to the right), you will be able to just barely see the small hole in the swingarm. It may have a slight yellow coloring to it. It's not easy to see, but once you find it, you'll know what you are looking for and find it immediately on subsequent looks.
Here's what I did to patch it: I took the bottom length of a coat hanger and cut it with the cutter portion of my needle nose pliers. I then gripped the end of the hanger portion with the needle nose pliers and made a slight bend in the end of the hanger (about 3/4"). I took a small piece from a cardboard box of MGD and cut a small rectangle of the cardboard. Next, I super-glued the piece of cardboard to the bent portion of the hanger. This will give you a small flat area to put an ample amount of sealing material on and use it to spread across the hole. I used Permatex #66B Clear RTV Silicone to seal the hole. I put a good size gob on the cardboard and I put on 3 quick coats to make sure I had a good seal. It helps if you have a small flashlight that will fit into your mouth, unless of course you have someone else there to hold the light for you, but I'll bet the light in the mouth will work better than trying to direct someone else to the small zone you have to hit with light. The total process from start to finish was about 10 minutes, and that was only because I wanted to wait a few minutes to make sure the super-glue adhered.
As far as why the holes are there in the first place, all of the theories point back to one item, which is that in the end, they should have plugged the holes, regardless of what they were needed for in the manufacturing process.
Here are a few photos to get you through. One other thing, doing it this way, if the MOCO does come up with something else, this is easily totally reversible by getting the silicone patch out. That's a normal wire coat hanger...I don't know why the photo makes it look so thick, so the piece of cardboard is probably less than 1/2" wide.