98 400 forks vs 99 400 forks

I just got a 99 400 and the forks seem like they are kind of rough compared to the forks on my 98 400. Both are stock. The 99 has new seals and oil (atf), I am not sure what fluid is in the 98. The 99 seems like it has alot more friction , when holding the front brake and pressing down. The 98 feels nice and smooth. Do new seals cause forks to feel this way before broken in? Are the forks on these two bike interchangable Are there any differences internaly? Thanks

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