So my only fear would be having the 10 years come due right in the middle of a major economic crisis when little to no money is available for refi.

I am not boasting/bragging but I am a bit offended that you would say such things to me when I seem to be having a nice measure of success in this business. 

I strongly suggest we dig up the 12 feet of pipe and replace it because evidently there are a couple spots big enough to where you will be having this problem every year with tree roots.Total cost, parts and labor, is $2,500 to:Remove and stack the bricks (there are bricks laid over where the piping is) but will not reinstall themDig up and replace 12' of 4" piping [he didn't mention what kind of piping] from clean out to septicPut copper sulfite at the joints to eliminate any risk of roots growing around new piping

As a side note, always take what the realtor says about appraisal with a pinch of salt.As for the converted apartment in the back, make sure that you won't be having any issue with the county regarding the use as multi-dwelling or not. 

I've read the Chicago RLTO summary and read enough posts here to understand his point of view.But how do I now ensure that the tenant will behave properly ?

We wouldn't be having this conversation without the freedom we're allowed.Like @Jonathan White said - maybe you can get a 2-4 unit with your VA loan and have your wife move into one of the units so that you meet the occupancy requirement.

I would think that most people here are Real Estate Investors and that everybody would be having the same problem as I am. 

SFH/SFR in the city do not behave like anywhere else in the country.

I think if you are planning to become a landlord ... then you need to start behaving like one.

Housing prices in Madison behave more like Chicago than they do the rest of WI.Peace!