- for the cash flowing in from my unit should I just keep a general checking account so it’s separate from my bills, personal funds, etc.?

You can perhaps pay for them separately based on each one's condition but this should be a blue book value, not an income-based value.

Sometimes the best deals you make, are the ones you don't, and I can guarantee you this, when you start rationalizing, or getting emotionally tied to a property, you're heading downhill from that point forward.Not enough info ($$$$$ numbers) to really even understand the true/complete picture here.

Also, I would be very surprised if your best strategy for generating revenue isn’t to rent the two units separately.  

If they send a "home run" deal out to a hundred investors or so then more than likely the emotional bidding will strip out all the fat off the bone with the only folks making money are the lender and contractors.  

I believe it helped separate me from other buyers as the seller stated that it was definitely a very unique technique.

Can I use 1031 money(from the sale of SFRs) to purchase commercial land, build a business on the land(using separate money) and then lease the land to my business?

If you don't have one, then emotions may take over and lead to bad decisions being made.

As I just advised my friend there is a cost to selling, but make a business decision, not an emotional one, pencil out the whole thing all the way down.

If you think you will need more than 10 notes in a personal name you will want to keep them separate.