I've had quite a few mini trucks. a couple 20rs, a 22r, 22re, 3.slow, and a 3.4l. The 3.4 is by far the best of the group as far as both reliability and power goes in my opinion, but that doesn't seem to be an option for the vehicles you're looking at. For wheeling, I'd go with the 22re. The 3.0 v6 is a much better engine for cruising down the highway at 75-80mph. It really does that well. For a daily driver I think you'd want the extra power. They do have head gasket issues. The cure: replace them. It doesn't seem to be a design problem, but rather something in the manufacturing that had issues. I have not heard of many that have had head gaskets replaced having problems. My 89 never had a problem. It always ran great.
For teh wheeling, I think the 22r is a good little motor. It's got decent torque at low rpms, is fairly fuel efficient, especially at trail speeds. I've never gotten better mileage from any 4cyl on the highway than i got from either of my v6s. I have not owned a 2.7 4cyl however. Anyway, under 50mph or so where you're not overworking the little engine they seem to do great. On the highway at speed I think they are just out of their efficiency range. The 4cyl's I've had would keep up with traffic most of the time, but there certainly wasn't power to spare. The 20r engines with 4speeds were better on the highway than the 22r's with 5 speeds. Not sure why, but I've tested them side by side many times with friends and the 20rs were always faster. That may also have been partially due to the first gen trucks being a little lighter I'm not sure.
On the trail the 22r or re does great. I think they are a fantastic motor for that purpose. The only issue I had were clutch problems as the clutch is small and can overheat. The solution for that is gearing. Dual cases and low diff gears are a must. For a budget crawler, I'd go transfercases first before axle gearing, but if you want to drive on the highway much I think you'll need both. Just the axles with 5.29's is not low enough for most crawling work. You will burn through clutches like crazy. Trust me, I did it.
I would not try to get much out of performance upgrades. My last minitruck was an 84 and I had the engine bored and rebuilt with mid-high end parts with a cam and the typical stuff. Anyway it would rev on up to around 8k rpms. Never had a internal failure, but what good does that do you on the trail? none. For the money you would be better off to buy gearing or replace with 3.4.
Those are my opinions. As you said, you plan on longer highway trips. I think you would be happier with the v6 and replace the headgasket. Or find a high mileage 3rd gen 4runner with a 3.4. I just don't think you will like the highway with a 4cyl 4runner. Take them for what you will.