Hi MF, seems ur problem with the VF-1D is same with what I was facing last nite. I just opened my 1/60 Hikaru's Super VF-1J, and after I attached the leg armor in jet mode, and after installing the leg armor I found it was really hard to unpeg the leg from the main body. After carefull jigling, I managed to bring both leg down for battroid mode.
Then I want to transform it to battroid mode, and that's where I'm almost frustrated by how tight the intake peg is! Afraid to break anything, I try to loosen it much like how u loosen your tooth from its socket, left n right, and suddenly with an audible CLACK! , I succeeded...phew! So I agree with ur assumption, might be the peg was too tight fitting...