A few of the challenges we had to face on this project were: keeping the historic exterior paint color, white with unique teal trim.

We also painted all the walls, doors, and trim.

Completely redid flooring, painted inside and out, new appliances, fixtures, fans, doors back fence, added back porch, trimmed trees.

That would certainly look more upscale than laminate.Is there anyway you can trim the budget from somewhere else?

It would trim about $9K off of her total interest payments. 

He also randomly pointed to areas of "flaking" paint around the trim of the home and window trim on the second floor that were "too high up to test" so it must be "assumed that they have lead paint" and we needed to hire a de-leading contractor to scrape away and remove these random tiny spots of "flaking" paint.

The additional panels and trim add significantly to the cost.  

In any case, storm windows over a well painted and caulked window trim can almost equal the r value of double paned windows and it matters little because glass is a terrible insulator whether single paned or triple w argon.

It also included replacing some damaged trim around the dormer windows, and some minor repairs to box gutters (box gutters are a physical part of the roof and soffit structure).So my quoted amounts might be replacing both your line 1 & 2 items. 

Purchase price: $77,000 Sale price: $109,000 House hack, no upgrades other than a little interior paint to cover up some oil stains and repainted the trim to the backdoor, and we put some mulch in the frontyard around the tree and under the shrubs.