Clutch linkage not lining up in neutral after shifting into 3rd

Used the alignment tool, everything works peachy until I shift into 3rd (I can shift back into first and everything is back to lining up again). New linkage/bushings.
My thoughts were to either adjust the 3/4 rod 1 turn without the alignment tool (or the 1-2 rod) or tighten up the stop a little?