Question for you auto transmission guys, and Crash since you
You want the add on cooloer in line with the one in the radiator because you still want some heat in the trans fluid--you can kill a tranny by running it too cold also.
Yes--you want the stock filter to stay in place. Sediments(clutch/steel/bushing) will setter in the pan and can easily be disturbed--you want that protection from the filter. Personally I would not run a secondary filter--I have never seen the need for it in the hundreds of trucks I see a year.