This is an old problem, since weapon specials were introduced. There is, likely, no solution to directly dictate weapon specials for custom weapons in such a way as to homogenize them with existing weapons. Many coders more adept than you or I have tried. It's something hard coded into the client and tied to a discrete ItemID.
There's 9 axes, which are just redundant swords weapons. You can replace any 4 and do no damage to players who want to use an axe. They'll still have more options than a player who wants to use thrusting pole arms, dual wielded 2h weapons, etc. Shepard's Crook is a weapon no one uses, many of the small hammers are redundant/useless as well.
There are many cases that justify replacement, if you're going to take the time to go custom. You can also make peace with your custom weapons having two good abilities. If it's really vital to the experience of your shard, focus your energy on building a custom weapon special system. I believe there's one in the resources area you can examine. It's not terribly difficult conceptually.
You could do something like grouping weapons by type, and giving each type an array of abilities. Bashing weapons can do X, Y, and Z. While slashing weapons to A, B, C, etc. You could use the existing specials, and add more without being limited by the hard coded book. The blade cuts both ways on that one. If you were to solve this enigma and assign new specials to custom weapons, you'd still be limited by the hard coded gump.
I don't begruge your drive here. I've added about a dozen custom weapons, and ultimately went with the replacement route for about half. I think disarm and paralyze are actually mid to good abilities, especially if you have a moderate population of armed humanoid mobiles.