There is a thread about overheated motors and G540s here. Where is your resistor placed? Is it on the connector that plugs into the gecko, or is it close to the motor? If it's the latter, then you may have the problem the thread discusses.
I think the power supply you have is adequate.
The home/limits issue is perplexing; I know I had lots of confusion at first.
You can, if you want to, and set up Mach correctly, do it with one input. You would have a combined home/limit switch on one end of each axis, and a limit switch on the other end of each axis. If you use mechanical switches, they are all wired in series. All this takes is to have Mach configured to home each axis separately, which is the default and configure combined home/limit (which allows Mach to override limit when doing the home operation).
You didn't say if you had a 4th motor for a double Y drive. If you do, then there is a good reason to have a separate input for the home of the 4th (A) axis; it allows Mach to square the axis when homing. On a smaller system, you only have one motor on Y and this doesn't matter.
I don't think there are really good reasons to use more inputs. You commonly see that people do use one input per axis, but the advantages are pretty small, and if you can use those inputs for more features (like a touch plate for example), I think it's just fine to combine all the home/limit switches.
I do like the electronic (hall effect) home switches. They are very accurate and repeatable. I have 4 x 4, with two drive motors. At the moment, I am using 4 inputs, but I'm going to move down to 2 inputs when I build a real mounting arrangement for my controller & power supply.