mayay, how long have you been in photography vs in the business?
It seems to me that your photography skills may be adequate (said without having seen any of your pics), but that you suffer from less than adequate customer and business skills.
A few recommendations:
First rule... HE WHO PAYS THE INVOICE SIGNS THE CONTRACT. Accept no substitutes.
Second rule... ALMOST NEVER refund money. Offer services in compensation, but no refunds unless it is something blatantly your fault.
Third rule... Be the quintessential professional. Getting lost is your fault. Visit the locations at least once beforehand. A cheap full size GPS on the market goes for ~$175-$250. Microsoft Streets and Trips comes with a USB powered GPS and software that installs on your laptop for about $99.
I would never go into a job blind. The pro that I shadow goes a MINIMUM of once to each location and often goes twice if he is unsure or needs to get more info. He also goes at around the same time of day as the event.
Concerning Timing, learn to roll with the flow, BUT... I see the value of shooting the formals starting with with everyone there, and then removing people until I am left with only the B&G (the people sent away go to the reception and since you are left with the B&G, once finished with them, you go with them to their Grand Entrance, it is therefore, IMPOSSIBLE to miss!). Best way to do it, and also the fastest... but again, it depends on how good YOU are. As am example, I've seen 250 KEEPER pictures taken in 60 minutes by ONE person well organized and who knows how to direct the traffic. We're taking 250 FORMALS only!
Seems to me that you were also "told" a lot and were often lost before the event started? Did you not meet with the couple in advance and KNOW the sequence of events? Late or not, there is an order that would have been followed that you SHOULD have been aware of and therefore been able to stay 1 step ahead of.
Expectations: Was it not detailed in the contract or a separate SIGNED paper the "must have" formal shots in writing? It was your responsibility as a professional to ask and finalize this list, and to deliver. If you did not do so... you may have painted yourself into a corner.
A big mistake was verbally agreeing the contract with the B&G and then letting the mother sign. This opened you up to a world of hell.
Mostly, I see a series of beginner business errors that all put together gave you a wedding-zilla.
Perhaps you need to spend some time talking to more professionals and see how they do it and how to protect yourself. Join the WPPA and talk and learn to professional wedding photographers.. Consider taking a course on business and customer service excellence. Your photography may or maay not be incredible... but EVERY WEDDING YOU DO will end up the same until you learn the business end of the game properly.