I've come to the conclusion that the more basic the solution, usually the better. Everything in the civ2 engine evolves around the cities and the terrains, so the more you can simulate using the cities and city/terrain improvements -and their effects on happiness, income/economy, science, trade etc. the better. Much better than units. In civ2, units are actually only the surplus of a society used to build a military. So if you need to simulate constraints on the military, point one, economy should be bad.
I've solved the "supply problem" so far with a combination of really bad terrain, a lousy economy, and severely limited government (despotism).
Jungles have no food, yet some particularly productive spots (firewood). The expedtion will need to found a few stations, or alternatively conquer villages/cities to get money for research. Without research they won't get more of the units they need to get past certain obstacles (like move pass ZOC's in difficult parts of the jungle). The terrain is slow and mostly poor, and units are quite vulnerable to sudden attacks. The tricky part will be finding spots which are productive enough, while able to supply food without constant civil disorder and starvation (things nicely covered in the engine), and provide defensive strongpoints. The more aggressively the player plays, the more units will be lost, and the greater the need for production. Building ones own camps will probably be more productive than conquering each and every city on the way, since the expedition lacks the techs that make temples etc work, so there'll be massive disorder, which must be disciplined first.
Porters are very expensive units, that can be disbanded for production. But they are unbuildable, limiting their supply to those given from the outset, and they will be much needed for new forces once the expedition reach the objective cities. I still have to figure out during playtesting which unit attributes are needed, to make it desirable to keep the porters as long as possible. But the "arrival" of the expedition triggers the rifleman tech, that allows riflemen to be built.
Units that can be built underway (depending on techs gained), are local escorts (of different sorts), steamers, canoes, captive women & children (pathfinders), interpreters (spies), and when the expedition arrives, riflemen and irregular troops to take the objective stations... "persuade them to be rescued"
I still use barbs and barb cities for the unusual encounters, but they are something that are met with suddenly and must be dealt with, not something you see move about on the map. I'm using the invisible city trick, and giving them very short range and high defences. So that it can be quite lethal to move around in the jungle without left-clicking every square before one proceeds.
-of course, cities and units make a ZOC, so they might be discovered that way too, but "in the path" so to speak they'll hopefully be a surprise!
Maybe you can use some of these ideas?