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Good work so far. To fill the small gaps around the windows, use a thin bead of Micro 'Kristal Klear', or PVA glue, and wipe off the excess with a wet finger. It should 'sink' into the gap, drying clear, and can be painted over.
Looks pretty good so far. I actually really like the gear struts and am not sure why you're dissatisfied. I don't recall the post talking about the Rapidograph pen but if you find it, please share. As to the sanding in the recessed hole, have you thought of just cutting a circle from very thin card and gluing that over everything?
Wonderful kit. Got one sitting in the stash as well so it'll be interesting to see how this one comes along.
A little hint regarding the clearparts on the front end of the fuselage. I do hope you've dryfit the clearparts as they have a particularly bad fit on these Revell HE-177 kits. The fuselage and clearparts will probably need considerable trimming in order to get a half decent fit on the clearparts in the front.