You have misunderstood how the lemon law works. The engine and transmission do not count as two strikes. You would have to require three fixes for the SAME PROBLEM with one or the other.
In Alabama, much like in other states, one of two things has to occur:
1. Three or more attempts, ultimately unsuccessful, to fix the same problem.
2. More than 30 days total in the shop, again to fix a single issue.
In either case the first repair must occur during the first two years/24,000 miles. You get refunded a prorated amount of the purchase price based on 100,000 miles.
No doubt if they can prove abuse they're off the hook. I suspect it's not hard for a manufacturer to avoid a lemon law claim on a manual transmission.