1996 Ford Contour Flex plate repair

I'll try to make a long story short. My check engine light came on and my regular repair shop replaced a couple of sensors (air intake (?) And one to do with the exhuast($500)-sorry do not have paperwork with me. During all this, they found its not running on all 4 cylinders and the timing is still not right-they tested the cylinders and found all are good. And also found a cracked flex plate. They have had it in 2 days trying to figure what's wrong(w/o having to replace flex plate) and finally have said they will probably have to take out transmission and relace flex plate.I am wondering what you think an estimate of that repair might run. They still havent gotten back to me with what their estimate is, but I wanted a general idea considering the time they have already taken with it - I really dont want to have to pay for 'extra' labor and I have no idea how time(labor) consuming taking out the transmission is. If you need more info I will try to help. Thank you so much. Grace