This is quite the departure from normal forum posts. Usually the forum is used for advice, feedback, documenting progress, etc. That means posting before turning the project into kindling.
I don't see anything in this project that wasn't fixable. More work than buying all the parts from Warmoth perhaps, but less than building from scratch.
Set necks are roughly matched to bodies, true enough. But roughly match necks often need a bit of work to be fitted to their "matching" body. It's also not uncommon to replace a neck on a set neck guitar...which involves pretty much the same fitting work. I am actually impressed that PB would be willing to ship you a new body. That comes at considerable expense from Australia. I did not like the quality of a kit that I ordered from a US supplier and had to pay the shipping to send it back to them. A replacement would have cost me shipping both ways.
At a similar price-point the quality from US suppliers is similar, quality control maybe a touch worse since PB has pretty regular contact with their suppliers. I certainly have not found US suppliers to be more accommodating. The folks at Fretwire were as good as those at PB, but the quality was no better. Other suppliers including the folks at Warmoth have terrible customer service, but I can't fault the quality of their necks and bodies.
This post will be of little value to DP, I suspect, but to any US resident who read it and is thinking about sending away to Australia for a kit... These are good value kits, and customer service is as good as one could expect given that it is on another continent. PB will even inspect your kit before sending if you ask--and I think you should. (Ask that of a US shipper and they will tell you your kit is boxed in a warehouse in another location, and that you should be prepared to eat the shipping if you need to send it back). Once you have your PB kit, use the forum, like the rest of us do, to help iron out any building or finishing issues you run into. it's best to do this before taking an axe to your axe.