Ask the driveline company how they want the measurement to be done.
I'm the king of measure 20 times, cut once and it's still wrong so I was worried about screwing mine up too.
Mine was a TKX so the length isn't applicable but I just pushed the trans yoke in until it was touching the rubber boot but not squishing it. Then I measured center of the yoke u joint center to the u joint center of the rear yoke. When I got to the driveline shop the guy did a little of his own math from my measurement and it fit just fine when they completed it.