Fortunately we have 2.5 drivers with stick shift knowledge (the .5 is me - I am guessing driving a stick minivan at my age is substantially different than cruising on a twenty year old saab at 19
)
No worries, I was in the same boat but it's like riding a bicycle a skill that never gets lost, and the modern manual transmissions are very smooth and forgiving. I just find the amount of traffic, lanes, and signs in Europe/Germany a bit daunting coming from Canada. So on the first day and drive from airport I take it VERY slow, and try to plan a route that is not popular. Also try to avoid rush hour traffic.
Does anyone know if there are substantial wait times in the Germany-to-Czech border, or especially in the Czech-to-Austria border?
It will depend on when you go there and what route you take. On the autobahn Muenchen-Salzburg there can be huge jams that last for hours, in particular during summer school holiday weeks. But there are plenty of country roads that cross the border, and there are many advantages to taking the scenic route and have less stress. Navigation systems can be set to avoid autobahn ...
In Czech republic be aware that there is zero tolerance to drinking an driving ... also all European countries have different rules for various pieces of safety equipment (e.g. reflective vests), and the rental company will only provide what is required for where you pick it up. So I tend to supply some items myself when I cross various countries.