Here's the stuff I can think of, mostly internal related.
The early cam has slightly less lift on the exhaust than the late, but is also the same profile as the turbo cam. They are all interchangeable and the late NA cam can be installed in an early NA or any 2.5L turbo for a slight performance increase. The early cam bearing/distributor flange used a smaller camshaft oil seal as well.
The oil pan gasket heat shield on the exhaust side changed a couple times from not having one to having a large one but the mounting holes stayed the same. My replacement motor was an 86 and had holes drilled for the bolts but not tapped. It's a good thing for the oil pan gasket if you can fit one on.
Main bearings are fully grooved up to about mid 84 I believe, but can be fitted with new replacements which are grooved only on the upper half. I don't know of any reason to upgrade to the later style if the original ones are still good unless you're maybe building a race motor. Generally, solid bottoms will support more power.
Early conrods were sintered up to Feb 84 according to the FSM and used different nuts. The early ones are smooth surfaced and are NLA. The later cast conrods used a ribbed nut. The nuts must not be mismatched to the type of rod.
Pre and post 85.5 oil pumps are supposedly NOT interchangeable.
Balance shaft rear bearings and housings changed a couple times but are largely irrelavant as balance shafts and housings should never be swapped between motors. I believe the front bearing/flange parts remained the same and are interchangeable. Correct me if I'm wrong.
Balance Shaft Oil Seal Replacement
The oil cooler housing from 87 onward has a flush surface around the hole where the locating boss on the oil cooler fits and uses the plastic spacer that comes in the oil cooler gasket kit. The earlier housings had a raised lip, sort of a built in spacer, and
do not use the plastic spacer or the oil cooler may be damaged when the housing is torqued down. This is very important and is not mentioned on clarks-garage. I'll have to write him with the page out of the FSM.
The aforementioned oil pan/pickup tube/baffles differences. It's always good to swap over to the later combination if you have the opportunity.
The oil pressure relief valves but that looks to be covered.
The halves of belt covers from manual tensioner motors and spring tensioner motors are not compatible with each other. Either all one type or all the other, and I believe spring tensioner covers will work on manual tensioner motors, but not the other way around...at least not without some modifications.
The coolant temp sensor for the dash guage is different, but the hole in the block is the same. Early electrics can work with the later sensor by just plugging the spade connector onto the larger lug on the late sensor.
There's lots of little external engine related stuff like fuel and intake, as well as the different DME and AFM between pre and post 85.5, but most of that I'm not familiar with the details of.