I would check the PivotWorks website to see if the swingarm bearing kit is the same for the '93 and '99 KX 250 models. If so, then the swingarm should bolt between the engine and the frame without issue.
I would also check to see if the Pivotworks linkage kit is the same for those two bikes. Even if it's the same, the length of the two dogbone links between the swingarm and the shock-mount link (L-shaped, runs between the frame, shock, and dogbones) might be different and throw off the head angle one way or another.