...but now the second engine is having some other major concerning issues, it stalls and backfires even after having it tuned by an expert( water jacket issues? Not sure).
Stalling and backfires aren't a water jacket issue. Those issues are probably a timing problem of some type.
Assuming the "expert" is competent but failed to check, might be worth checking your cam timing and make sure the timing chain didn't skip a tooth. If so (and it hasn't crashed the valves) it's just a timing chain and gears to fix it, not a full rebuild.
Just bring the number 1 cylinder up to top dead center on the compression stroke and see where the timing mark is. There are tricks to finding the compression stroke, like putting your finger in the spark plug hole and turning the motor until it puffs at you. Then bring the piston to the top using a wooden dowel or something to watch it.
Not saying there aren't other reasons you could be having the issue, just tossing it out there.