For the first item, I would try out CMD-Command. It really is a nice disk manager that copies files easily. My 4040 had no issues with this but in CMD-Command, my 4040 was identified as V2. Could that be DOS 2? If you bring up CMD-Command and choose your drive (the "D" command) you will see your drive identified. If you have a 4040 drive, is yours different?
Second, I'm just not sure what's supposed to happen when BASIC loads. I assume I'll see another screen where there's a BASIC editor/environment?
I appreciate you setting up your SuperPET. I am still in awe of mine even if it's a bit temperamental right now.