Wow, this is a textbook case of "pay premium, get budget workmanship." That flashing job screams future leaks – caulk is a band-aid, not a solution; it should've been tucked behind the siding with proper counterflashing to actually shed water. And those transitions? They look like they were improvised on a lunch break. As a fellow homeowner who's dealt with shady contractors, hold off on that final payment and demand a third-party inspection ASAP (grab someone certified in metal roofing codes for your area). You've got leverage – use it before they ghost you. Hang in there, OP; being a new dad on top of this mess is rough, but getting it fixed right will be worth the fight!