I got all crazy this winter and installed one of those metal lowering boxes for the trolling motor pedal and I wish I hadn't.  If you stand up all the time when fishing it is a great thing to do.  But here are some of the setbacks I and my partner found after using it for a few days.

1.  You have to adjust your old stance when you are using the pedal. The way you used stand doesn't work anymore.  Your feet have to be farther apart and your weight evenly distributed.

2.   You may have to adjust the way you cast because where and how you stand is now different.

3.  If you sit down you will never get used to having to use your heel to get the motor to spin around to reverse.  The angle at which your foot is at on the pedal (when in reverse position) is so extreme that you can't push down hard enough with your heel to make the motor spin.

4.  The setup diagram shows that the incline angle goes to the back.  I tried it this way but it kinked up the steering cables and I couldn't hardly steer the trolling motor.  So I turned it around and it solved that problem.  But, now I can't get the heel of my shoe to go inside the metal box so now I can't push down with my heel to go into reverse.

5.  The metal box is so large that it will set your pedal position back about 3".  It also takes out about 8" x 13" of deck space and it limits you to having to stand exactly right there all the time.

I had to put (2) 2x8x10 inch boards under my pedal in order to get it to work correctly.  So I am having a 1/4" piece of Aluminum cut to cover the hole and I will put the pedal back on the deck.

Quite a lesson to learn for about $200 in parts and 12 hours in labor. :'(

I hate to hear about your problems.  I have just the opposite feelings about the flatfoot which I have on my deck.  It makes standing or sitting a lot more comfortable and is a lot easier on my knees and back since I am standing line a person instead of a dog taking a leek.  I have had it for 2 years and wish I had done it a long time before that.

Man I dunno about that.  IMO it dosent look to ergonomic, and takes up quite a bit of deck space.  I have a Minn Kota with power drive, and sometime ago put the Minn Kota Co-Pilot remote on it.  It is probably the best thing I could have done.  No deck pedal at all, just a little bitty remote.