Is it possible you put the ground glass back in backwards after cleaning? The thickness would be enough to cause back focus errors. With the later Speed Graphics that had Graflok backs and the focusing ground glass holder which is designed for the Ektalite field lens (Fresnel) the order of surfaces starting from the inside of the camera is smooth side of Fresnel, etched side of Fresnel, ground side of ground glass, smooth side of ground glass, your eye.
place your focusing frame on a flat surface, rear side facing up. measure the height of the inner edge of the frame that the gg sits against. if it's 3/16", you have a frame that's meant to just have a 1/16" gg with the frosted side facing down. you can as an option add a fresnel on top of the gg without affecting focus. if it's 2/16", you have a frame that's meant to have a 1/16" fresnel with the grooved side facing up and a 1/16" gg with the frosted side facing down on top of the fresnel. if the fresnel was replaced with a thinner one at some point or installed wrong side up or swapped with the gg that could explain your focussing issues. you can leave out the fresnel with a 2/16" high frame as long as the gg is 1/16" thick and installed frosted side up with some extra padding between the gg and the clips holding it in place.