im no expert, martian may answer your question alittle better knowing a few things.
1st off, what are your pot values, capacitors, and or resistors.?

2nd, maybe could be your pickup height, whats the recommended height, what height do you have?

try raising or lowering your pickup heights.
for a while i was having issues with cs 69s, in the middle position sounded muffled, or low tone.
i adjusted the pickup height, i remember thinking "what a few turns of screwdriver affects on tone is cool"

_________________
"Yesterday is history, tomorrow is a mystery, but today is a gift. That is why it is called the present."

oogway, kungfu panda 2008

They are fatter than vintagey pups
and I noticed a little loss of highs/spikeyness
but not 5/6 on a tone control diff

You can try raising up the treble side of the pup, that will help
Lower the bass also for balance

Some adjust pups by lowering them very low ....
Then bring the treble side up to get the highs you want...
then raise the bass side to taste
Many have the treble side higher than the bass side

What values are your tone caps?

I have a set of Fat '50s in an ash-bodied hardtail and they sound perfect with that combination. The caps in that particular guitar are .022mfd. You might try playing around with the values to improve the tone.

HTH

Arjay

_________________
"Here's why reliability is job one: A great sounding amp that breaks down goes from being a favorite piece of gear to a useless piece of crap in less time than it takes to read this sentence." -- BRUCE ZINKY

1st off, what strat did you replace the pus in? we may be able to help you out.

_________________
"Yesterday is history, tomorrow is a mystery, but today is a gift. That is why it is called the present."

oogway, kungfu panda 2008