Obviously the throttle linkage on the valve cover has to be removed in order to adjust the valves. Lots of opportunity for something to get disturbed that could affect the transmission. Could be the Bowden cable or some of the vacuum components. I would check the Bowden cable adjustment first. As far as the valve rattling is concerned, the valve clearance is excessive when the engine is cold. Does it continue to rattle when the engine is at normal temperature?