The lease includes a clause that allows us to annually increase the monthly rent by the amount of annual increase of property taxes.

Can we just indicate the garage will being used by us in the lease agreement?

You inherit the lease and responsibility unless the contract states otherwise.

Lease says tenant pays 1/3 of the utility bill.

So property management, dealing with rents in some capacity, being a floor manager in college, showing an lease on a room you rent out in your current home...anything along those lines to show you have experience of SOME nature will be required when purchasing a multi-unit property with a VA loan. 

Also, they could write a lease to you, then have you sublease to others.

Our lease states that we do not guarantee parking lot spaces.

You have to prove to the IRS that has been an investment property by showing a lease. 

I know that I’ll need to confirm rent rolls and validate each lease.  

I'm assuming (and hoping) he hasn't actually signed any lease with you yet nor have you given him keys.