Are there any methods to buy these properties since others may be leary? 

I always recommend a legal professional - you can ask questions and though they are more costly, should provide you with the answers you need to feel secure. 

I'm an investor in Massachusetts and I'm curious if there's a creative way to set up the landlord/tenant account that holds the tenant's security and last months rent deposits in such a way that the annual accrued interest can be paid to the tenant automatically...As of right now I'm required to manually send a check to each one of my tenants on their year anniversary.

Therefore, you father (the executor) will need to work with the IRA provider in having them update the your uncle's IRA to list the name and social-security-number  of the beneficiary of the estate (not your uncles name as he simply the executor). 

Assuming you have a decent job and reasonable credit score, you should definitely be able to secure better terms through regular conventional financing.

Both methods are tax differed and give you AMAZING returns. 

I have fully paid off my primary residence and have secured a HELOC of $435K against it from US Bank, secured a month ago.

Fortunately, you have the security deposit if it comes to that point to help cover some of the costs. 

I didn't really know about so many different methods of investments that exist out there....  

That's both halves of medicare and social security, so 15.3% in total.