My turn signals started acting funny. Both indicators coming on when I turned on the left signal. I started to look and I found water in both front turn signals. After blowing them out I find one more design flaw. Where the wire come through on the top water can run in. I am going to get some silicon and fill the area around the wires and see if this does the trick.
Anyone else have this issue??? 
Yup, and it's been that way for a lot of years. Water enters through the lens to housing joint every time you wash the bike or ride in the rain, and even though the reflector has a rubber seal between it and the housing, water can still enter between the bulb and the socket. A good bead of dielectric compound around the bulb will help with that issue, but it's still a good idea to pop the lens off and clean the contacts and the socket on a regular schedule along with your other maintenance items. BTW, all that moisture will tend to cause the yellow paint on the Harley bulbs to blister and fall off fairly quickly. Find some real natural amber bulbs, not cheap painted bulbs.
The second place the water enters is the one you mentioned, where the wiring enters the bracket. That is just a total botch job by whomever designed it, and I've noticed that the MoCo has done nothing to change that even though this problem has been evident since they first started using these mounts. I've done the same thing you are planning, adding some clear silicone sealer, but I found that just doing it while the parts are still mounted on the bike isn't necessarily effective due to the tight access. I got one side sealed, the other continued to leak slightly. I eventually took the brackets off the bike so I could get them sealed completely.
Jerry