How can I identify where boxes of misc nuts and bolts go on my 3.6 rebuild?
 

When I picked up my engine parts from the mechanic nothing was organized or labeled so I have no idea where what bolt goes with what nut. Is this just an extreme puzzle Im going to have to put together or is there a way or method to identify what Ive got and where it goes?

Have you looked this up in PET? It lists the fastener sizes for nearly all assemblies.

I used the info in PET, plus a lot of photos I took, to re-assemble one of my cars after I sent all the hardware out to be re-plated.

The easiest thing to do is separate and count the items you know or recognize
There is specific items and general fasteners.
Nylocs nuts are used outside the engine and spring washers and regular nuts inside
Thick aluminum washers are used in 2 sizes on valve covers, chain box covers and oil line caps going to cam oiling.
Post up what you don't know, there really isn't much left.
Bruce

sounds like solid advice thank you