I have yet to run across a PS-2 5V engine that has the boards installed in the engine that I could not install the PS-2 3V in the engine. (Including RJR Mountain) I have installed 3V boards in all the Bantam engines, various RK and Premier engines.
In my opinion it is always better to put the board in the original location and retain all the extra features that presents.
I would not bother ordering AE-15/16 as MTH doesn't really have anymore of them. What they do is have a tech remove the connectors on the AE-10/11 and install the 5V versions. Just slows your order up, since you can do it with the old 5V parts.
Plus if I want bent pins on the board, I can do that myself
As far as changing the battery 2 pin, you do need to do it if your placing the board in the engine with battery in the tender. Since the engine 2 pin is a 5V variety. Otherwise, you can leave it if the new harness is being used.
On a side note, I have even installed the battery or a Super capacitor in some Premier engines that required the new board. This makes the engine independent of the tender except for sounds, and frees up a wire or 2 for additional tender features.
For some other manufacture PS-2 Upgrades, I place the board in the engine when possible. Example the K-Line Hudson. This allows for more feature control on the engine. It does require different harness. G