There are two screws in question, 55589-S2, 8-32X1/2 hex sems, and 55590-S2, 10-24X1/2 hex sems. My Oct 65 San Jose 66 Fastback uses 55590-S2 (10-24), my May 65 San Jose 65 Fastback uses 55589-S2 (8-32). This size problem came up for me last month on a friends two 65 San Jose Fastbacks he's getting back on the road, one an Oct 64 build, the other a January 65 build. Both use 55589-S2 (8-32). The 65 Body Assembly Manual (page 47), rev date 4-22-65 (barely legible), shows 55590-S2 (item J) but no reference as to if or when it was changed. This may be another "use existing inventory first" situation. I cannot verify if my 65 Fastback trap door is original.
Jim