Then, subtract your expenses. 

Should I subtract the expected income coming from the "other" section since the storefronts are currently empty?

I’d like to invest into rental properties long term, and I understand the process of taking overall revenue and subtracting my liabilities, (insurance, taxes, cap ex, repairs, vacancy, mortgage if there is one etc).

But generally you can take your Monthly Gross Income lets say $1,000/month and subtract your debts (i.e $100/month car, $100/month student Loan...) leaves you with $800.00/month. 

Will the bank still "see" me as owning all the equity in the house or will they subtract the loaned amount before calculating the LTV. 

By subtracting the debt balance from the value, they can see what your equity position is on each property, and combined.

Subtract the estimates from the AFTER rehab value.4.

After this, you subtract out certain adjustments to your total income (many people won't have adjustments here).

If I know that, then I can subtract my repairs and closing costs and give a cash offer that would be based off of debt coverage ability ensuring I get my investment back in full.

You then work backwards subtracting repairs, other costs to acquire, hold and resell (I call them the soft costs), and then your expected profit to come up with a purchase price that makes sense.