Caboose cleanup.

Hobby plastic sheet; cut to fit for a plug and modeling putty used like bondo on the gaps/imperfections. Putty can be found next to the modeling cements in the toy isles of dept. stores or a hobby shop.

Imperfections can be minimized some while adding strength by mixing super glue gel with plastic "sawdust", shavings, or baking soda. Much harder to sand smooth though ;putty is best for the final surfacing.

Very minor imperfections may fill in with paint or filler primer. Though the latter may wipe out detail, spoting/masking/sanding can cure that.

Here is a similar edge blending. It has a backing layer and finish layer filled at the gap with red putty (there is also grey, choose as you would primer color, or alternate colors to see high/low spots easier as you sand and finish with red or grey depending on topcoat choice.

Backing the windows then plugging them may be easier for you...? 

Thanks guys. I'll have to pick up some modeling putty and give this a try.