The 1% of purchase price is a good rule of thumb, but you might want to consider seeing what similar units on the market are renting for in that area. 

In general, would a 3BED 1BA house appraise higher than a 2BED 1BA house, assuming both houses are the same in every other aspect? 

Data rules the world, and unless you are in a large city, the chances of having enough data at a high enough speed is rare. 

Namely, a duplex that can cash flow (0.9-1% rule) and appreciate (~5%).

.$145,000PURCHASE PRICEPurchase Closing Costs$2,000.00Estimated Repairs$20,000.00Total Project Cost$167,000.00After Repair Value$170,000.00Down Payment$7,250.00Loan Amount$141,882.50Loan Points$4,132.50Amortized Over30 yearsLoan Interest Rate5.400%Monthly P&I$796.71Total Cash Needed$29,250.00Monthly income:Rent:$3,500.00Other:$0.00Total operating expenses:Mortgage expenses:Vacancy:$350.00Repairs:$350.00CapEx:$350.00PMI:$40.00Garbage:$20.00Insurance:$56.00Management:$350.00P&I:$796.71Property Taxes:Total Monthly Income:$3,500.00x50% for Expenses:$1,750.00Monthly Payment/Interest Payment:$796.71Total Monthly Cashflow using 50% Rule:$953.29I made conservative estimates on everything.

I do realize that I would be up against the clock with the 1031 IRS rule if I sold so I would have to have some properties lined up before I did this.Lastly, I do have someone who seems to be willing to give me advise (mentor) with my deals.

Big takeaways Asking Price: $145,000Gross Rent: $2,500 (some of the units are below market rent so I'm assuming I can raise rents to at least $625 a unit)Cashflow: $169 (This seems awfully low for a quadplex considering it's much better than the 1% rule)Any advice would be greatly appreciated!

Again, your local buidling code will rule the day, but Missouri falls into Zones 4 and 5, which would require R-49 via the IRC. 

I read that California and Florida have different rules than most of the country.

I don’t care how you want to try and justify or rationalize it, it is what it is.