They are very similar in certain ways. The Super Distortion is ceramic magnet, more punchy (primarily low-mids), crunchy, and more output. The Holy Diver has less output, but the distortion character is more smooth and saturated like a JB. the Super Distortion gets a little messy and harsh at higher gain levels, but Iron Maiden levels is fine. The Holy Diver can handle higher gain just fine, and it is very clear, organic, and the string to string separation on a chord is amazing. (You have one so you know). Super D has pretty good separation too, but the more gain you add the worse it gets. So they sound similar, but you get a more flexible contemporary sound with the Diver.
I consider the Holy Diver to be a good half-way and improvement on the characteristics of the Super Distortion and JB. You get the tight rhythm sound of the Super D with the more singing quality of the JB for leads.
You can't go wrong with the Super D, it's still an extremely popular and great pickup, and one of my favourites. Be careful with the Charvel though. Is it one of the newer Japanese Pro Mods with the direct mount pickups? The pickup cavity is too shallow for a Super D (it's a very tall pickup because of magnet size) so it would have to be routed a bit to fit. I ended up leaving the Duncans in my San Dimas because they sound perfect in it. I didn't like Holy Diver in the San Dimas, but again I didn't take the time to get the height right because of the direct mounting.
I would say the Super D would be more suited to your Jacskon because of the basswood body. The Super D tends to overtake the wood with its punch and power. But only as long as you could properly fit the Diver close to the strings on the Charvel. With a Pro Mod you would need to shim it to get it high enough, the Diver is shorter than the JB. If I were you I would just leave things the way you have it. The JB is perfect in the Charvel.
