Everyone has their own opinions on these rigs. Suffice it to say people do a ton of wheeling and overlanding/expedition travel in both and they both perform like champs. I own an ex-cab '98 and a d-cab '03 Taco and my family is just the wife and I, so I removed the back seat entirely in the d-cab and there is a lot of climate controlled storage space there. I designed and built a custom topper for the bed to solve the sleeping quarters issue and we enjoy a comfy queen-sized self-inflating air and foam combo matress that works great. Also, the RTT's are fabulous additions if you are a truck guy and don't get the runner, but you could put one way up on the roof of a runner, the tradeoff being a higher COG than having one at bedrail height on a truck.
I have tried to sleep 2 in a runner, and have found that sleeping on a platform or RTT over the truck bed is nicer, roomier and does not require moving all of the gear out onto the ground and into the elements or into the front seats every time you want to go to sleep like you do in a runner. The wheelbase issue goes both ways as well. Some people like the shorter WB of a runner. Personally I love my longer wheelbase Tacos because I rarely lift a tire in the spots where the runners and FJCs have a foot of air under one. And the greater ground clearance of the Tacos over the runners helps to keep the breakover angle pretty similar even with the longer wheelbase. So in my mind, advantage Taco. Also you said the Taco has a rear locker, runner is open/open then for wheeling ability, advantage Taco. Same 2.7 motor and 5-speed in each, so its a wash unless you look at the gearing of the diffs, unfortunately without looking it up I can't tell you which model came with lower diff gearing, if they are not the same.
Most of it comes down to personal preference. In the end, if you don't have stong feelings about things like wheelbase and storage/sleeping issues, just go with the one with lower miles on the odo and go from there. Last thing regarding power with the 2.7 and running something like 33's... regear the diffs, whichever rig you decide on. You will not regret it. Oh, and post up pics as you build it up!