I believe the investor may need a commercial loan at that point or could do 3 separate loans since they are on different parcels.

I proposed the question if the separation of funds was for asset protection.  

Question 2: Is it a good idea to put every piece of property into a separate LLC entity (1 for 1) or is it okay to put a few properties into the same LLC?

I am now under the suspicion that their friend, the one who is still living at the property, is the one who created separate accounts for all three of them and did the signing for each individual who is under this lease agreement. 

You can simply request a separate check for the $100 increase to bring the total deposit in line with the new rent amount.

Another idea could be to see if the HVAC system can be adjusted or modified to better separate the airflow between the units.

Separately, the benefits and disadvantages of renting to Section 8 is a topic of extended debate on this forum.

we just managed to get ong to run all new lines and separate meters for our whole apartment complex at no cost to us. 

I have so many questions though.1) Can anyone tell me more about series LLC and whether it's necessary to hold each property in a separate LLC2) What are your thoughts on a trust, rather than an LLC - advantages, disadvantages etc?

Ideally you would want to transfer the funds you expect to use for the purchase to your new entity for your records to create the separation from personal to business.