On the rear end feelings... A rear sway bar is pretty much mandatory on the extended vans, especially when towing. Otherwise, body roll as actually inducing bump-steer, because of the geometry of the steering setup.
Have you verified the tires are Load Range E? An insufficiently stiff tire is no good for handling, and if it's not an "e", the rear tires would be almost certainly overloaded. Likewise, running the max 80 psi is almost mandatory when towing, depending on weights of course.
Definitely get that trans fluid changed out! That few miles with that many year means it's pickup up a lot of moisture over the years. While it sounds like you finally cooked that off, the oxidized compounds will still be circulating. The "bucket method" is my preferred way to do it, and it's super easy once you cut the cooler return line, and install an inline filter there after the fluid swap.
You're cold-start issues could be a number of issues. One quick test you can do is unplug the MAF. If it goes away, replace the MAF. After test, you might have to look at the IAC next. Of course, with the current age, plugs definitely should be swapped. It's always hard to diagnose an intermittent problem, when there's some deferred maintenance that could also cause similar symptoms.
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2000 E450 dually V10 wagon
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