I don't know what Jack did here but I would make the template by using whatever method works for you. I would take three pieces of wood with a perfectly straight edge , and use clamps and double sided tape to stick them down. Next, put the neck in and get them adjusted so they are correct, then rout into the template material with a pattern bit.
Another method I've used is to print out the neck cavity to 100 % scale and glue that down and put the wood on top of it on the lines.
As far as the holes, you can take pointy things and stick them into the existing holes to transfer the hole locations into the body. Sharpened dowels or similar, or even some cut nails that fit.
One thing to note is that if the neck fits tight, you won't be able to adjust the E strings to the neck and they could fall on one side more than the other. You want a little wiggle room...not a mortise and tenon fit. But there are those who insist and want a press fit for maximum tone transfer and other BS...so it's up to you.
I would just add that the way I do it is I leave the holes as a last step in the process - my templates do not have holes in them. I make the neck/body templates so that the neck fits into the heel just tight enough to lift the guitar up from the top of the head to about 45 degrees (this is a little on the tight side - but it's what I like). Then, when I fit them together I take a set of 4 screws that would be the same size as the neck screws , cut them to about 1" and screw them into the holes so that the pointy end is poking out about 3/8" (or if you want to make holes in the neck - screws that fit about 1" into the body holes). Then just fit the final neck and body together and use those holes as the starts for your holes for your body (or neck as the case may be).
As Marty mentioned ^^^, One last step is to drill the body holes just a little bigger than the neck screws and then take a slightly bigger bit and counter bore the neck and body holes by hand just a bit to help to make sure there are no little bits of wood that might make them not fit completely flush inside the heel.