Adam, sounds like you have some legitimate concerns that need to be addressed even if your municipal inspector lets it slide.
My advice would be to hire either an experienced carpenter that would be willing to work with you to correct the issues before the framing inspection or find a sympathetic home inspector that is willing to go above and beyond to help you fix the issues before the red tag goes on from the municipal inspector. Of course you could also get a structural engineer to design a fix.

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Jim Luttrall
Mr. Inspector.net, Inc.
Allen, Texas 75002