Which kit are you building? Is it the Tamiya 1/32 kit? If so, I'm in the middle of figuring out how to deal with the main gear as well. I think I have come up with a good solution, but the end result will tell the tale. I left my main gear off, and haven't glued the center gear well divider in place yet. That just leaves the wide-open gear bay and the fire bottle to mask off, which I did with a combo of Tamiya tape, Scotch Blue painter's tape, and then Silly Putty to cover up the final, fine, irregular details. Hopefully I'll be able to put the main gear assembly together, glue in the center divider, and use Milliput to close up the gaps at the front and back of the divider, while still leaving a visible panel line and have it look like it was meant to be. I use really thin coats of paint, so its really easy to make an invisible blend with parts added later. For underwing stores, I paint hard points and stores off the model. I'm thinking I'll mate the wing tanks with their hard points and then paint the subassemblies off the model. For missiles, I always paint those and their hardpoints separately. You can either carefully scrape the paint from the attachment points for the missiles and use Tamiya orange cap cement, or you can just attach them all with epoxy which works well (but its a PITA trying to get them to stay in alignment for the amount of time it takes the epoxy to cure). As far as a sequence goes for attaching the missiles, I prefer to attach them while the hard points are already installed. Just lay the model on its back on a towel to protect the paint, and you can use its weight to keep the hard points relatively steady while you have both hands free to attach the missiles.
Here are a couple of pics that sort of show what I'm talking about with masking the entire gear bay.
