I had the same problem.... Here is a functional fix I use. For the downtube that is too large in diameter: Borrow and use a large Visegrip locking pliers. Bigger sizes are a necessity. Use it to squeeze the downtube in the area underneath the forward engine mount just enough to form it just under the diameter of the engine mount. I recommend you use work gloves when clamping down. I kept pinching my hand skin everytime I clamped down (lots of pain and foul words!). Now, the gloves get pinched. You are going to have to clamp and squeeze repeatedly to move the tube walls a little at a time. Use lots of liner (paper towel tube, maybe) around the downtube to prevent excessive paint being scrubbed off. The result will be a slightly oval tube, top to bottom, with the top and bottom curve of about the same diameter of the engine mount.
To fill in excessive gap between the engine and the downtube (optional): Get a set of JB Weld 2-part epoxy. Wrap a layer of wax paper around the downtube where the engine mount will settle. Hold in place with a clamp holding the paper, the clamp dangling underneath. With the engine on the bench, prop it so the engine mount surface is facing straight up. Put a little "fence" around it with electrical tape. Wrap the studs as well. Mix a large blob of JB Weld epoxy on a sheet of wax paper. Popsicle sticks are good at this. Place the well-blended blob into the engine mount fence. Give the epoxy some time to harden from sticky liquid to a clay-like texture. Then take a few minutes to mount your engine into its final resting position on the bicycle frame. (The electrical tape will kinda fold under; it is unavoidable.) The epoxy will form around the contour of the downtube, eliminating gaps. The excess epoxy will be squeezed out. Let it sit undisturbed for 12 hours or more. The wax paper will allow you to remove the engine back to the bench. Pull that off and toss it. Pull the electrical tape off and toss. Use a utility knife to trim off the excess expoxy. The end result should be a non-compressible custom contour to your downtube.
I found it necessary to double-nut the old too-short studs and remove. I replaced them with Grade 8.8 bolts, 50 mm or longer. Ace Hardware carries a nice selection of metric 6mm bolts and nuts. There should be no more side-contact problems.
Mike