It definitely provides better steering when you mount it on the stern, but then that opens up a whole can-o-worms about controlling it with it way back there, especially if you're doing a DIY design/install. There are two things you could do that would avoid major customization headaches.
1. You could always get a tiller extension handle with a u-joint. I have one of those for my squareback canoe and it worked very well. Then all you would need to modify is adding a cable to the lift lever so you can get it up/down in the water when needed.
2. You could just get just get a sidemount and put the trolling motor on one side or the other right behind the seat. You could also put it in front of you on a sidemount (and then reverse the control head on the shaft which is easy enough to do).
If you still would rather do the whole custom stern install (which I do understand because that's what I did for my kayak), just know that it's not anywhere near as easy the two options above. Although I did go the stern mount route, I just ended up buying a pre-fabricated kit including the motor from Island Hopper Outboards. It was expensive, but it was pretty easy to install since I didn't have to reinvent the wheel. Since you already have a motor, you could buy their motorless kit, but even that is pretty pricey (like close to $300). For my stern install I opted for a long tiller style steering control rather than foot pedals. I did this because my kayak isn't exactly rudder ready so it would've taken some extra work to rig up steering pedals, and plus if I'm standing I can't steer with pedals.
Also, for a battery I use two of these in parallel (making a 12v/70Ah battery):
https://www.amazon.com/gp/product/B00KA ... UTF8&psc=1
They're 24lbs each and much smaller (7.68 inches x 5.16 inches x 7.13 inches) than a normal marine battery. They're sealed and spill-proof, so you can mount them sideways if you wanted. I actually store them in the front hatch of my kayak and then ran the wires through the hull to the stern. Note that if you're going to do something similar you have to use a really heavy gauge wire or the wire will get REALLY hot in use, which would definitely melt your kayak hull or even cause a fire. The easiest (and cheapest) thing to do is just cannibalize a set of jumper cables. I've taken the kayak out with the motor on some 6-7 hour fishing trips, motoring around most of that time including using the trolling motor to keep me in place/positioned when I didn't feel like anchoring, and I've never been below 75% when I put the batteries back on a charger. Depending on how much you actually use the motor (and how long you're out fishing), you could actually get by on just using one of these little batteries.
Hope this helps!