As for the getting back to the transmission cooler and thermostat for controlling the temps.
First - The standard way people install auxiliary coolers. From the trans to the stock radiator based cooler; then to the aux cooler before going back to the transmission.
Second - The item in the middle with "Endcap" pointing at it is the thermostat that opens at 160 degrees fluid temp. This is one acceptable way to install the thermostat and is commonly recommended so as the aux cooler only adds
cooling capacity when the fluid really needs to be cooled back down to preferred temps. When temps exceed 160 degrees the thermostat sends fluid through the cooler to cool it back down. When the fluid reaching the thermostat is -/= 160 degrees the thermostat closes so as to route the fluid back to the transmission.
Since we have 3rd gen 4Runners we have the pink milkshake issue and commonly bypass the stock radiator so as to avoid this issue. Hence I will run this setup. Out of the trans to the thermostat where the fluid will be routed back to the transmission as long as it is under 160 degrees. Once fluid temps are =/+ 160 degrees the thermostat will open up and send the
trans fluid to the external cooler and make use of the B&M 70266 larger cooling capabilities. (I am trying to find where I found that the NPT fitting B&M coolers do not have the internal cool fluid bypasses build in.)
Sorry about the MS Paint skills - it is early and I need to go pick up my supercharger housing so I can finish rebuilding it today. I'll try to check back asap.