Bally - the best solution is to fly the a/c! With the trackline available is is so easy. IF you must fly in auto, do as you say - programme r/w c/l +20nm as WPT1, next WPT on the route as WPT2. As you approach 3000' in LNAV, ask other pilot to select new WPT and execute at (or just before) 3000'.
As for Q3, I cannot see how you can have all these 'waypoints' in the way? Can you explain? As oak says, unless the waypoints are in the SUPP database, they clear after 'weight on wheels'. Otherwise clear them before startup.