Line by line, my responses are in
bold.
Are the transmissions you referenced automatics? I want to keep my truck as an automatic even if I get rid of the A4LD.
No, they are not. I have not spent much time around the A4LD, but from what i understand, they are less that 'good.' I do not own, nor drive automatics, so definitely not the right guy to ask 
If I can’t find front and rear sway bars on a B2, would buying aftermarket sway bars for B2 to put on the 89 automatic work?
Possibly. I know of two front sway bars for TTB RBVs, the behind the axle variety, and the before the axle variety. I do not see where the before the axle variety would differ from truck to truck. I may be wrong on this. @85_Ranger4x4
You suggested changing the 89 Ranger intake to a pre 85 Ranger intake. Will any pre-85 intake for Ranger or B2 with a 2.9L do?
So, in order to avoid confusion, there are a few different throttle bodies for the two main flavors of 2.9 intake. The earlier 2.9 RBV upper intakes had a large bore throttle body, and the later had a small bore. I believe 87-back has the larger and 88-92 has the smaller. A larger throttle body on a mostly stock engine will feel more responsive on the throttle.
What modifications can be made to the air box or the tube that begins behind the grill to the air box? I noticed what appears to be wires/sensors on the tube at at midway union.
The rain cover at the front is rumored to be a restriction. When I still had my factory air box, I removed mine. Can't remember if it did anything. Take a look at the tube connecting the air box to the grill, and see if the tube is more restrictive than your throttle body.
Where can I find ‘regular’ JBA headers for the 2.9L automatic? I see them for a 2.9L manual on their website. What do you think of going from a Y to an H exhaust on the 89? Difficulty?
No idea. Mine came from a clearence sale on eBay. Also, exhaust is one of the things that I farm out to a local place. I'll do under hood work on an exhaust system, but not the rest. Too much rust in my eyes for my liking.
What other vehicles besides the Windstar have the 3G alternator and harness? That upgrade may be one of the first I do. With that done, I could move on to other electric upgrades.
I believe most of the 3.8s had the 12-6 o'clock mount tabs. One of the ford techs on here will know more than I. But essentially any 12-6 alternators will work with the Chebby bracket.
I see that you used MB electric fans. Does the brand matter or will fans from other vehicles work just as well? Any preference with regard to sizes on either side?
I actually have three - one eBay cheap-o rigged up inside the factory shroud, and the now-removed MB fans out front. The front ones were removed to fit an intercooler. E-fans are sort of a self-contained mod. Most of the offroad guys will recommend a kill and manual override switch fitted to them as well. From personal experience, the override switch can be a lifesaver when your thermostat fails (happened to me)
Is there an Explorer rear axle that is the same size as the 89 Ranger rear axle? I’ve read where there axles are wider/longer and the rear tires protrude a bit and may require different size wheels. I’m big on symmetry and want to be able to rotate tires at will.
Expo 8.8 is slightly wider, but axles are same bolt pattern for wheels. Just a much beefier axle versus the Ranger 8.8. AFAIK, every Ranger/BII axle is interchangable, just a matter of having the correct u bolts, top plates, and lift blocks.
Thanks in advance for your input.
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