You might also want to add a pint or quart, if there is room, of transmission tune up. This sometimes helps with problems like you mentioned and is recommended after fluid and filter changes.
Rick Kilpatrick, AAS Automotive Systems Tech, Alamance Community College, Class of 99. 06 5 speed manual Mustang with Pony pkg : GT Mac Mufflers, true duals with one custom pipe. 2.5" system. GT bumper cover, all installed March 7&8 2006. AFE Stage 1 CAI, Motoblue Underdrive pulley, GT aluminum shifter knob, honeycomb rear blackout panel,and dash kit installed. Roush hood scoop and side window louvers installed. SS taillight trim has been installed, new alum. GT steering wheel installed.