When I had the two JTV's at the same time, I was using my first FRFR with my Helix, a DXR12. This was before high and low cuts became common knowledge, and I was fighting high end sizzle and artifacts. The maple neck JTV seemed to exacerbate the problem more than the mahogany neck JTV did. It wasn't a huge difference, but every time I would A/B them back to back with the same patch and settings, the maple neck would seem a little brighter. This was always using the same strings and a Variax sim, not the mag pickups. The only other difference between the two guitars was the maple neck was a short Gibson 24 3/4" scale length. I don't know if the scale length had any effect on the tone. Anyway, I sold the maple neck JTV and kept the mahogany neck sunburst. That neck is a standard thin profile and still feels really good in my hand. Plus I like the bubinga fretboard. Before you change necks, you should experiment with strings, because they do make a difference, especially if you changed brands as well as gauge. I remember that the stock neck had very nice acoustic tone and good sustain. It was just a little too bulky for me. Good luck.