yes, those are pin supports... they are just to position hard top, i don't have them so every time i need to adjust hardtop on all ways to fit correctly. miss 1mm and windows will not close correctly and will have problem with leaking.
about that cover, mine was in worse condition, cracked all around. so i remove completely it because it could tore soft-top window. also try to bend straight as much as possible, some guys are putting long tube where window bends. because bended like yours could break and snap especially in winter. bend with no angles.
btw:
http://www.facebook.com/profile.php?id=642458248
this guy is also parting barchetta, maybe have what you need. he is from Belgium.