Increase the rent by $100/month for dogs.

Quite often, wholesaler A sends me a property and a few days later, wholesaler B sends me the same property but with a slightly increased price (including his fee).

Then start doing flips, buying notes, tax liens, and more to help increase your capital while the rentals provide a foundation to rely on in case a fix and flip goes bad.By the way if you plan on managing the property yourself, try using a service like cozy.co or something similar.  

Fifteen year lease with annual rent increases and lease backed by corporate.

If you are trying to do both cash flow and appreciation then you may want to sell it in the next 5-10 years and realize your increase in value and this would be more difficult in a "run down" property and it may not appreciate as much anyway.Another thing to keep in mind is that a more "run down" property will attract a less quality tenant which can create more stress and worry.

They gave loans to people who couldn't possibly repay those loans, especially when their adjustable rate mortgages increased. 

Although I do plan to sell within the next 3 years (military orders) I want to make sure I didn't make a terrible mistake by lowering my payments now just to save a few hundred dollars but increasing my total loan.

Even if the claim is valid they will generally deny the first time paying out and make you work for it as they know statistically some of their customers filing a claim will quit the process if they make it hard on them to be successful.The insurance industry  is for profit and they will try almost anything within the law to make a buck.

Downside is split single contract into two, double closing costs and increased mortgage insurance costs.MY QUESTION:Does this sound correct, or is the underwriter mistaken...Do multiple townhomes require their own individual loans for each single unit (even if apart of the same structure)?

The property needs about  $400k in repairs to increase the ARV to 1.5 mill - 1.7 mill.