Custom home builds seem to get killed by appraisers. The biggest factor that the appraiser will never admit to is there is no purchase price pressuring them upward so that a sale can go through.

That being said I believe there are things you can do to influence the appraiser. I made sure I was there when he came. I walked him through my house and pointed out the valuable upgrades and what they cost. I told him at the beginning and the end of the appraisal what number I needed (with another 30k added in for wiggle room). I was really nice but a little pushy. He came back 20k under what I told him and it worked out fine.

Good luck