There are always additional items that come up.

Is there any way of removing negative items on your credit report before they expire off.

These are two completely separate line items and should be keep that way.  

These other items make it worth using a 1% agent vs. a flat-fee guy where they just put it in MLS and you have to do all the negotiating yourself, but that's not worth thousands of extra dollars to pay 3% commission.

In a fee per item you would be paying for that phone call.

I go to different stores and buy data directly from them, and I also pull from the big 3 bureaus.

The appraiser will remark on these items you are talking about and if they are not in really bad shape, the loan would go through normally. 

The Bigger Pockets book store if full of great books: https://www.biggerpockets.com/store

But remember their standards are lower, so be careful not to spend money on items that a B class would require. 

Familiarize yourself with how the return was prepared, what items were put on what form.