Our readings at the DTC connector are as follows: CAN bus Hi pin 6 2.09 V, CAN bus Low pin 14 2.75 V. Shouldn't this Hi pin read the high voltage and both together equal 5 V?
You can't measure this accurately with a plain multimeter, you must use an oscilloscope. It's a high speed digital pulse signal. The "high" in CAN High means that it goes high=3.5V in case of a dominant bit. Whereas CAN Low goes low=1.5V in case of a dominant bit.
Either signal idles at 2.5V. In case the bus load is low, both signals would measure close to 2.5V if measuring incorrectly using a multimeter. You won't get 2.09V at CANH ever and you won't get 2.75V at CANL ever. You are measuring this the wrong way or you are using the wrong tool (again, use an oscilloscope).
Measured the resistance at the CAN bus, with battery disconnected; we are getting 45.6 Ω between pin 6 and 14. This should measure 60 Ω. Can not work out why it is ready that low, has anyone seen this before?
The most common reason for that would be that there's voltage present when you are measuring. But it's also not that important to have exactly 60 ohm on most vehicle applications since they have relatively short distances. I often plug in my CAN listener lab stuff onto an existing terminated CAN bus and then I could be adding 1 or even 2 additional 120R terminators. Out of experience, I (non-scientifically) know that going below 60 ohm is rarely a problem (assuming some <20 meters of bus) but going above it could be. One would have to dissect a CAN transceiver in-depth to tell the reasons why, but that's another story.