RG, I have the same set up as you: 12ft on a trailer with a 5hp 4-stroke. As the manual and other have said do NOT tow with the motor tilted up as it could pop loose and drop/smash down, and that angle puts a extra stress on the transom. If you need to tilt it up for clearance from the ground then make sure to use a transom saver bar.
The lowest point on my outboard's leg it 14 inches off the ground (when on the trailer). I have not had any issues with clearance. That being said befroe I back it into a lake I always tilt it up just in case.
I also bought a heavy black rubber bungy cord that I use to give the motor extra stability when towing. I just strap it across the back of the boat and over he back of the bonnet. It keeps the motor from twisting from side to side.
Also another good idea IMO is to buy a outboard lock. They go over the bolts that tighten the motor to the transom, making it a real bother if someone wants to steal your motor. Yes if they really want it they are going to find a way to cut/break this lock, but it is a good deterant and makes your motor less of an appealing target,. I got mine from Cascade in Chilliwack.