Looks like you're doing the BL first, which is good. That way you'll have plenty of clearance when you're lifting the motor and transmission for the MML. Otherwise, you may have to lift the tub to get enough space to get the motor mount bolts to line up with the MML installed.
For the MML, if you can't get the through bolt out on the driver's side, remove the entire bracket holding the motor mount to the engine block. There are three bolts at 45 ft-lbs. Be careful with the bolts if you have to work harder than that to get them out so you don't strip something. Once you have the entire assembly out, you can put it back together with the through bolt coming in from the other direction.
The nut on the underside of the passenger-side motor mount can be tough to get to because the bolt holding the bracket to the engine block can be in the way. If so, you can pull that bolt while you're working on the motor mount nut and put it back when you're done.