It looks as though if I were to use Arduino I have to get rid of the bootloader and step back into the world of printer ports and DOS command lines which I thought I'd left for good.
I'm not sure I understand this comment. What have printer ports got to do with it?
You said it was working, and now it isn't. Quite possibly you broke it. There are a few things to consider. There is a maximum current you can draw from one pin, and a maximum from a group of pins. Also a maximum for the chip in general. These are documented in the data sheet for the device. Also if you happened to be testing a motor without reverse protection diodes you may have blown something.
This site documents a number of ways (10) you can destroy your chip:http://ruggedcircuits.com/html/ancp01.html
However to be fair, you can destroy any
chip if you are not careful. Personally I haven't destroyed any, and this includes after I have been drinking.
You can throw your Uno out the window if you want to. And then in a couple of months you might be throwing out your Microchip evaluation board.
I have a number of them sitting around my house doing things like monitoring if the garage door is open. I have to say that they are completely reliable.