All of the "Transmission on endpoint 2 failed (err = -109)" messages typically indicate that the PK4 wasn't fully updated.

There are three parts to the firmware inside the PK4, and whenever you change MPLABX versions it's important that all three sections get updated to match the version of MPLABX you're using. This applies to a PK4 right out of the box since there's a good chance it was built with a different set of firmware than the version you're trying to use (you'd think a brand new one would work, but no).

This is supposed to happen automatically, but on all the PC's I've ever used it doesn't... each time you open MPLABX IPE it'll update one part and then hang. You have to let it timeout, close MPLABX, reopen it and it'll proceed to the next part. It takes about three or four whacks at this until it finally loads all the firmware and magically everything works. During this process I've seen MPLABX produce almost every conceivable bogus error message you can imagine.

That's why you'll see a lot of posts about rebooting, unplugging the tool, closing/reopening etc. It doesn't always happen quite the same way, but for me it's been this way since day one with MPLABX and ANY of the programming tools. It's even worse if you have one of the older tools (PK2, PK3) and you switch back and forth between the old MPLAB 8.92 and MPLABX.

It's a good idea to make sure the tool isn't connected to your target hardware while it does this dance, just the USB cable.