From my recollection bridge clearance on the Mississippi River is 54 feet and on the TennTom it is 52 feet. Shouldn't be a problem. The jumping Asian carp may be a bigger problem. They were not an issue when I did my river trip.

Passing through the locks is no big deal and after the first one you will get the hang of it. If some guy in a 14ft john boat can do it...you can do it. There is no charge...that's what we pay our taxes for.
If you plan on a mid May start on the river you may have higher water volume and current levels due to the spring thaw and rains. I did my trip in August when the river volume is likely to be lower. The actual level does not change a great deal in a
normal year except when the snow melts in the spring. During the summer the spillways are used to control the pool level between locks. With a wet summer the spillways open letting the increased volume through and also increasing the current. When it's been dry the spillways adjust to contract the flow slowing the current but always keeping a certain level in the pool. I think the current may have averaged 1.5 knots on my trip with 3knots the most we saw in Rock Island for a few miles as we passed through the city. But it can vary from year to year so my experience may not be your experience. You will have to see what the spring and early summer bring.
This last summer with all the rain the Corps closed the locks in Minneapolis to traffic and left them open to get rid of the high water level. The water flowing through the locks was like a Class V rapids as if ripped through the locks. Some of the locks further down were also closed for periods of time.
Once you get a technique down two people should be able to raise and lower the mast. I helped a guy put his mast up on an Oday 25 in Little Current one time. We hit it off and spent two weeks cruising in Georgian Bay. I don't recall the set up details but it only took the two of us. It may have involved the winch on the trailer and another support pole so it may not be as easy doing it on the water. I am sure there is a youtube video out there for your particular boat.
My friend may have already left for the winter but I will see if I can track him down.