Since you can't selectively choose which cutlines to use in VW (either all or nothing) then learning to manipulate cutlines is more of a issue that relates to learning the design software you use, rather than a VW issue. I only have experience with Gerber and Illustrator, but regardless of the vector software, they should have options to copy/paste (right in place) and then options to weld together or subtract from. It takes some getting used to, but those types of functions are critical to learn in this business.
Regarding the pausing issue, we had the same experience. Ultimately, in our case, the main board had to be replaced. A fairly common issue seems to be that the board loses connection with the on board ethernet port (temporarily). The expense with part and labor was maybe $2200 to $2400 I think? This issue, especially on a VP-540, seems to come up commonly on these machines when they get to 7-10 years old. If, when this happens, you look at the status of the printer in versaworks, it says "disconnected", it may help point to this being the problem.
It's possible that your issue might be something else, but I've seen this come up a lot on signs101 in the past few years with the main board being the culprit.
Feel free to message me sometime if you want to make the trip!