Low strings clacking high frets after setup...

[prater]

So I recently did a setup on my MIM Jazz Bass after switching to lighter strings. I reduced the neck relief a bit, (tightened half turn) then lowered the saddles because the strings were really high and made playing difficult. Got everything tightened up and adjusted to reduce fret buzz on the higher frets to a minimal amount, but there is still a bit around 12-15 but it doesn't come through on an amp.

Now however when I pluck the E or A string more than a feather light touch I get the clack sound of the string hitting the highest fret, I'm not plucking that aggressively, just a solid pluck and follow through to the next lowest string. There is no clack if I use a pick.

I'm also noticing some buzz from my low E if I let it ring out open, it will begin to buzz around the fifth fret after a few seconds.

I already assume the nut probably needs to be built up after the larger strings, but what would eliminate the clack when plucking. I've raised the saddles but it didn't do any good, any higher and the strings will be uncomfortable to fret.

Anyone ideas?

[Marty Forrer]

I'm sorry to say this, but I believe your setup is not complete. The strings need to be removed and the frets levelled and dressed. Possibly the fingerboard also needs to be planed in that area. Fenders are notorious for developing a "hump" in the fingerboard in the area of the neck joint. To do this means some of the frets need to be removed.
You really need to take the bass to a luthier for assessment.