I have a fuzz war clone and I run a cry baby mini after it. I think it sounds awesome but it depends what you want. I recall having the same issue as you which is why it's in that order.

I did try another wah when my original full size cry baby broke but it was even worse! That was a Morley lead/boost model I think, which just sounded shit with the noisy pedals I have.

I'm also running another couple of fuzzy things earlier than the fuzz war.. I think if I put the cry baby first it probably wouldn't work at all. Tbh all those pedals affect each other a crazy amount. I love the fuzz war sound but it's a pretty extreme effect as you'd expect from DBA.

Good luck with your experiments!

A lot of fuzz pedals will do this because they produce harmonics on octaves above and below the predominant input frequency. If you're changing that predominant frequency with a parametric filter, the fuzz is working hard to undo it.

The way I remember it, overdrive guys liked wah -> OD, and fuzz guys liked fuzz -> wah. You boost the frequencies you want to OD versus "shaping" the fuzz.

A different brand or model could do the trick. A more transparent wah will not be as prominent against a heavy fuzz or distortion. If you like the tone of the Fuzz War I would keep it and try other wahs.

Get a guitar with a whammy bar is what the old ones would say.