Thanks for all the replies.
I will try to answer all the questions.
1) I know a little or enough about electrical to injure or kill myself. Lol In other words I know the basics and don't have a lot of experience with it, only wiring light fixtures, receptacles and switches and the sort. Not wire tracing.
2) I do have a digital multimeter and a voltage tester.
3) Both conduits enter the garage on the same side between the garage and house and about 1-2 feet apart. I'm not sure what you mean by termination, (inexperience). I'm pretty sure the big conduit goes in the fuse panel for the garage and as for the smaller one, must be for the two lights at the front of garage.
4) I am pretty sure I tied the Neutral back into the switch. Did I do it properly? I don't know. lol. I will have to check it again. Also for all I know the old timer switch could have still been working fine.
5) All switches and receptacles has a function as normal with or without a switch. It is only this one switch that appears to do nothing and only one set of lights (front garage) that has no way to turn on. So put two and two together leads me to believe that those lights are tied into that switch.
I was thinking about getting the Sperry Wire Tracer for this problem, would this help in this case or do I even need it?