We went there & checked all the 'serious deficiencies' & many were minor. 

Not at all - What they are is a higher interest rate and they're going to look at you a lot harder.Basically (in a lien-theory state), they're limited to what the house is worth if they have a trust deed and since you signed, may have a deficiency claim, but ask a KNOWLEDGEABLE commercial mort broker. 

., inspect the mortar joints and bricks, if any deficiencies (holes) arefound we will patch the hole with hydraulic cement.

If maintenance visits show that the tenant is not properly caring for the unit, steps must be taken to put the tenant on notice of that deficiency if it will lead to higher repair times or costs.

Tell them it is concerning that they are not performing on the contract and they are not being truthful about the deficiencies.

@Daniel Rockrohr an inspector is trained to look for things that may be deficient in a house.

Yes if it was a good deal it is likely someone would have bought it, most likely scenario is you calculated incorrectly, but it could have a deficiency like mold, an uncooperative tenant etc. 

Should I just compute an average class-b cap rate across the US and then make adjustments for perceived features of deficiencies of this property in particular vs "the average".

If there are deficiencies the contractor needs to satisfy them before pulling the final payment.

especially in non deficiency judgement states.