Thanks for a wonderful write up!
I'm trying to use the sibling of your device, the TUF-2000B, which is in a waterproof case intended for wall mounting.  All the parameters and steps you describe, however, are identical.  
Unfortunately, I am finding that for certain pipe parameters and transducer choices I get a negative mounting distance (M25).  Do you know why, and what I can do about it?
A sample: OD=22.2 mm, wall=0.81 mm, liquid=water, transducer=TS-2, mount method=V  result in a negative distance -1.7mm
Changing to method W results in a positive distance = 18.3 mm

Hi, Great guide. I am looking into purchasing a TUF 2000-m. Would anyone with access to the control box be able to find the approximate transducer spacing for a stainless steel pipe with around a 4.5-inch(114.3 mm) and 4-inch pipe diameter (100 mm),  Pipe thickness of 0.25-inch (6.35 mm), using a V shape waveform using the TM-1 transducer and no liner? I am trying to get a range of the spacing for the transducers before purchasing the equipment

Thank you- very good description.
I am trying to set up my TUF-2000m.
I am having trouble getting a good quality reading. 
I have designed a 3d printed clip on adaptor to hold the TS-2 sensors to my 22mm pipe.
This should help with alignment. Keeps orientation yaw/roll/pitch constant, and allows me to micro adjust sensor spacing.
My Q value is poor.

I also note that if you look at the specification for copper pipe and its wall thickness, these have a tolerance. 
By trying the extreme tolerance values for the pipe in the TUF-2000 I saw a total sensor spacing variation of 0.57mm.
The actual spacing of the sensors may need to be adjusted to get an accurate reading.
Also note that the reaction of the TUF-2000 is not instantaneous, so calibration needs to be done after the flow reading has stabilized.
I move a bucket under the pipe outlet for 1 minute after the flow rate has stabilized and then measure its volume. 
I compare this to the flow rate given by the TUF-2000.
I came here looking for an answer to the temperature sensor. 
My TUF-2000 also reads 46C, but I notice this number does not change when I warm up the TS-2 sensors.
The TS-2 sensors do not have temperature sensing in them. 
You need to purchase two PT100 sensors (euro 4 each) and wire them to the TUF-2000 using pins 52,53 & 54.
I have yet to get my device to work to my satisfaction- but I keep experimenting!
Good luck with your.