A 50 year warranty and 5 year light commercial.

Sure, but you need title to tell you what they need for it to be a valid sale and recording. 

I sent her $5000.00 earnest money (to be refunded if the deal fell through) Then she told me I had to send her the rest of the money before we met to close the home plus money for a warranty deed versus a quit claim deed.

I feel pretty good about my numbers but do you suggest, I contact a realtor to validate my rental projections once the upgrades are complete?  

I believe it also comes with a warranty if the company installs but it will cost you more.

I was wondering if the appraiser does have a valid point or he is holding grudge against me for scheduling issue that occurred earlier. 

I generally file copies of confirmation of these notices in the county/parish courthouse under the property description and parcel number to ensure there is no future questions about validity of the sale.

They even threw in a 1 year seller-paid warranty and a $1,500 concession to reduce my closing costs!

They are also willing to settle the IRS lien out of sale proceeds at a higher price and transfer ownership via warranty deed.My question on the IRS lien is whether or not there are opportunities to settle the lien for a lower amount. 

They refuse to honor our warranty.