For serenity, stroke the check and chalk up the little bit extra to shared appreciation.  

Time will tell if they are worth the extra expense.

I don't cashflow in my owner occupied duplex... but I just about break even giving me extra money that I would normally be paying in either rent or my full mortgage.

House also doesn't have operable A/C...so I don't see any extra motivation to get this done "in the near future" with sweltering AZ heat. 

She had some extra furniture in storage that we paid to use for a short time.

Frankly if you have extra money you can keep that in the bank as a safety net until you feel comfortable enough with the income from that rental to then buy a second property.Most of my clients purchase with a loan but then as they generate income the revenue is put back into the property, through either improvements or paying down the mortgage. 

The clause mentioned is a prepayment penalty, where an extra percentage is paid to make up for it. 

I am looking at low down payment owner-occupied options through a portfolio lender at 5% with PMI, that will go away once reaching 80% LTV (so will get some extra cashflow after approximately year 7).In my analysis I account for Expenses including (common utilities, taxes, property management (10%), Long term maintenance (10%), short term maintance/repairs 95), legal, misc, vacancy (7%) etc, etc.)

Did you pay the extra and was it worth it?

This is a small home and I'm just using the extra cash to help me through college.