Scott, when you say you're having trouble with control, do you mean actually operating the motor, or the way it propels your inflatable?
Wonder if you could flip the head 180* and make a mount to put the TM up front (between your legs/feet)? They make a "big man" seat, you might look at.
When people mention rod holders, I never know if they just mean for storage (when moving between spots) or for actually fishing. Either way, you could add a rocket launcher style holder on the back of the seat, and one on each side (of the seat bottom) for easy/quick access when fishing.