DCinLinnCo,
The Tower Trainer you are building is the same one that I learned to fly with, and still have hanging in my garage so I can use it instruct with. I have 200+ flights on this plane, so I'm pretty familiar with the entire plane in general.

You are correct about the engine mounts. The holes drilled in the mount are there to use a strap of metal to bolt down the engine. If those straps are missing, you can replace them fairly easily by visiting your local hardware store. you need two straps of metal long enough to extend between the pre-drilled holes in the mount and 4 bolts/nuts long enough to extend through the mount. to mount the engine you place the engine on the mount and then fasten it in place by putting the straps of metal over the engine's mounting lugs. then use the bolts to tighten down straps to hold down the engine. Make sure you get self locking nuts, or use thread lock to make sure the nuts don't loosen and fall off due to engine vibration.

I prefer to use the strap system of engine mounting on a trainer as opposed to drilling the mount and directly bolting the engine on. This way you can experiment around a bit to see the effects of engine thrust on your plane. Just another use of a trainer, to teach you the different effects on engine thrust.

I've snapped a quick pic of my trainer so you can see how the mount should look.

Hope this helps.