I guess those parts aren't actually glued in just yet. Does that gap close up with gentle pressure? If so, I would leave it as it is and let the glue hold the joint tight. If the gap persists, and if it was me, I would try and figure out where the points were that were holding the piece away from its seated position and ease those a bit to see if you can close the gap (as Warspite suggests). If not, have another go at making the ill-fitting pieces. With the knowledge of where the gaps are, and their size, a tight(er) fit should be possible.
But - it's your model, your call. It is a fair bit of work you will be ditching if you start again. And it's always worth looking for unintended consequences - if you make a piece very slightly different from the plans, will that impact on the fit of other pieces later on?
Good luck with the fix, however you do it (or don't, you could just live with it!)
Greg