In the case described by the OP, I think that taking the ap out as soon as the a/c is stable, configured and trimmed is a good idea. Don't try for a super slick stable at exactly 1000agl. You could brief the CM1 that you want to be stable at 4 miles so you practice the visual segment. After the ap is out, very little control input is required on a reasonably calm day. Then concentrate on the papi's to train yourself to look outside and not worry too much about the instruments (PM should be monitoring the instruments), transfer your concentration onto the fixed distance markers at 200'. Which should take you down to the flare/ retard at about 20'.
This is a really common issue and is almost always down to overcontrol of the side stick.
If you are inadvertently overcontrolling when looking outside, consider making your grip on the sidestick very loose.