I have found a few multi-family properties I am interested in purchasing, all meeting at least my minimum cash flow numbers and Cash on Cash percentages, however these properties are about 4 hours away from my primary residence.

I have read about surcharging the residents a certain amount (maybe $25-50/month)  Do I just include that in my loan amount or can that just be listed in the lease as a separate expense for the tenants? 

Although you shouldn't need 20-25% down for an owner occupied residence. 

Fast forward my wife and I have new jobs about 45-60 minutes from our current residence.

We require all applicants over he age of 18 that will be living in the residence to have a background check and credit check ran (through Cozy.co) The daughter with special needs is over the age of 18 but morally I do not feel right making her do a background and credit check.

Or is it a complete / private residence for the man and his 17 year old son?

The way I understand the new tax law is that HELOC interest is only deductible when used to build on to, or make repairs to one's primary or secondary residence.

When we move out of our primary residence in 53222 we will probably be able to rent it for $1300-1500/mo.

Many time when you show up in person, it not only help build relationship but they also waive the fines, after all they are doing their best for their residents by accepting non paying job and trust me it is lots of work and time they all allocate.

We have two homes in Bozeman, MT that have been rented out for 7 years as well and are currently living near Fort Carson in Colorado Springs where we will be renting out our primary residence in 5 months when we move to San Diego for a 2 yr assignment.