Ok great, I've built a coulple of TL-1s. There are some links below where I have pics of lining up the neck and checking the scale length.
I generally get the neck seated nicely in the pocket and then clamp it and drill pilot holes for the mounting screws. Then temporarily fit it and use a ruler and the strings through the 'E' string tuners to make sure it all lines up.
If you are using a pick guard its a good idea to include it in this process.
https://www.buildyourownguitar.com.a...?t=8005&page=2
https://www.buildyourownguitar.com.a...?t=8291&page=4