It easy to convert it to a short shaft, you just need to find the parts.
You aren't stuck with a taller transom after raising it, reversing it is done by simply unbolting the riser and removing it, now you're back to the the short shaft length.
Drilling holes is a non issue, not even something to be concerned about.
You just stack the new plywood directly on top of the old transom, the only thing that overlaps down onto the old transom is the aluminum plate on both the inside and out side of the transom. This assumes that your current ransom is in good shape, if it's in bad shape you will need to fix what's wrong with it first.