Mr. Kauffman
Weclome to the forum. First, your questions can't be answered in the manner of which I assume you would them to be. Reason, the odds are that none of us here appraised your house and we don't know where you are located (it would be helpful to get better responses, if we knew where you were located - at least the state if not the city).
Next, water heaters, heating systems, etc., are all part of preventative maintenance. While you, as the homeowner, may consider it an upgrade, it is something that must be done from time to time. The "tilt in windows" are something that are considered, typically, to be upgrades but the market reaction is what the appraiser must reflect and work with - if there is little to no reaction (or market indicated data) then the appraiser cannot just pull a number out of the air and apply it - s/he must be able to back up those adjustments.
Now the basement is locally influenced factor. In fact, we have few houses in my area with basements. Also, per ANSI standards, fannie mae and other quasi-government standards and requirements, a basement is a separate line item factors and addressed on the report there. What the appraiser probably did was reflect a market indicated action/reaction to a basement. It's one of the same factors I mentioned above.
I have actually seen where a basement was a negative factor. Have you made an effort to get the lender to grant permission to discuss this with the appraiser? The appraiser must have the "client's (lender) permission" to discuss anything about an appraisal with anyone else.
Good luck with it.