If you are going to be fishing out of the front of the boat ( I reccomend you do. You get better control of the boat that way) you will see a screw just under the head of the tm that holds the head in place on the shaft. Take that screw out, turn the head 180* and put the screw back in. You transome mount is now a bow mount hand control. You can make a simple rudder for the rear out of a cople pieces if plywwod and some angle brackets and use a wood clamp to clamp it to the transom.
No issues removing the foam. I know guys that remove both the front and rear foam. The foam just keeps the crawdad from sinking to the bottom if you do happen to flip. The front foam is more then enough to keep that from happening. ( dont ask me how I know
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For the rods guys place the butts of the rods on the floor and have the tips facing to the back on either the left or right side of the crawdad.
Try and keep it a simple as possible with maximum fishability. Too many bells and whistles in my experience weighs the crawdad down and complicates things.
Also note the guage of the wire on the TM. Any wire that is added to make the connections reach the batteries should be the same size( guage) You can also opt to store the battery under the front seat instead of the back especially since you are going with a 12v ( one battery) tm.