Did your sharpie number look like this?
I bought a black 97' VJ off Ebay a while back. It had the same neck plate and bolts, bridge, etc, and a similar pickguard gap as the one in your pics. The main difference is mine had two string retainers, same as my 00'. I eventually got sick of the fingerprints and smudges and flipped the body on Ebay. The buyer had concerns regarding the authenticity of body due to the lack of countersunk neck bolt holes and a cheesy, visible seam in the 2 piece body. Thinking it might be Frankenbass, I emailed Modulus, asking whether the neck left the shop as a VJ or as an aftermarket neck. They confirmed that it left their shop as a black VJ. I also asked about the neck plate and lack of countersunk holes and they said they "did it both ways depending on what the dealer requested". It seems that somtime after, all VJs got the countersunk neck bolts.
I wonder if they outsourcing the VJ bodies of that vintage.