Sure they aren't cracked? Do they sound ok if you tap them with a screwdriver or something? Or that the nylon tipped plungers that strike them are broken or missing.

Is the game high tapped?

Are the grommets that the plunger(s) sit on when at rest still there? Sure that the new plungers are the correct length etc.? Though it's still hard to imagine how those would make the bells sound like a 'clank' instead of a ding or a dong. So if you hit 'em with a screwdriver handle or whatever, they sound fine?

I had a 1960 Williams Jungle. Super cool game and I still regret selling it. The one thing that grated on me was the damn bell in the lower cab sounded like someone hitting a metal coffee can with a hammer. I played around with it a bunch of different ways. Even swapped it out with a different bell and and never could get it to sound right. I think I decided it was just where it was placed in the cab was the reason. Maybe it's a similar type issue for you.

A photo on ipdb shows the two bells inside the backbox. Both are electrically operated bells.
Not sure if this is correct; one of the bells is usually a mechanical clapper type mounted under the 0-9 unit. Are both of your lightbox
bells electrical as in that photo?

"Diamond Jack" has a small bell mounted toward the back of the main cabinet instead of the usual position in the lightbox. I've heard many of them that sound more like a knocker than a bell. It's very difficult to correct it to sound like a bell, and I believe it's because of the location.

Perhaps it is adjusted too close, and during the brief time the coil is pulsed the plunger tip is actually rebounding high enough after the initial hit (and coil still energized) to lightly hit the bell again and 'kill' the ring? Would be too fast to see it actually happening. Just a theory though, can't think of anything else.