I don't know how much these differences create a issue with a swap.
Given the limited supply of original vehicles of the model years you are talking about, the age of such vehicles, I am curious just where you figuring to pull out one and have any reasonable expectation of it being in decent running condition?
Maybe you plan to rebuild one or are getting a crate motor, I think the basic blocks and stuff are unchanged from the whole BII/Ranger run from 86 thru 90 (and even up to 92 with Ranger). Some of the year specific items can be carried over in the swap.
I can't comment on how difficult a swap is taking any 2.9L from the 86 thru 90 BII/Ranger or up to 92 Ranger and putting it in an 86. There were engine changes between 87 and 88 (outlined below) and then gen 1 to gen 2 body style changes between 88 and 89 but I have no idea if the body changes really affected the engine compartment at all.
I think 87 and 86 are the closest engine generations. 88 definitely had some changes but using an 88 may just require a computer swap too.
Differences:
Throttle body changed port size between 87 and 88 model years. IIRC 86-87 had larger ports than the 88-90 years.
EGR was deleted between 87 and 88 model years. 86-87 had EGR which was used to keep the cylinder cooler to keep emissions in line (and possibly better valve reliability?)
86-87 used banked fuel injection while 88-90 used sequential fuel injection. I don' t know what the trades are here, but since I've heard mention of EGR delete and combining that with 88 computer swap without mention of wiring changes, this could just be a computer thing.
Also of note, is the cracking problems with the heads if engine got overheated. In 89 there were modifications, but this was just internal to the heads and doesn't affect anything else with the engine. As I recall the modified heads occurred in 89, but maybe it was too late in the year, but whatever reason not many BIIs saw the new heads. If you are swapping motors it would be desirable to have the better heads. They do fit the older model years.