I've also owned my share of vehicles.
(I'm at about 25-30 at this point.) For me, early Montero's and Troopers are solid rigs and I have no real feedback on those.
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The newer Montero's and Troopers 1995-2001 have some pretty clear differences.
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Motor
1. Firstly, the 2001 trooper I have has a smooth, powerful, reliable timing belted, non-interference motor. The 3.5l sohc in Montero SR's are interference motors. Snap a belt, and there goes the neighborhood.
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2. Montero motors have butterfly valves that can fail and basically turn the motor into a paperweight. No such failures occur with the trooper 3.2. or 3.5l motors
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3. Both motors use oil. that's a wash. In the trooper it's improperly designed pistons, in the Montero, it's valve guide seals. Neither are a big issue if you keep eyes on levels.
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4. Spark plug replacements on the Montero are ridiculously complicated. see this 6 part video for a taste of what's involved:
https://www.youtube.com/watch?v=SMtWHiPnISY
The reasoning is that one can use lifetime plugs. The thing is with an oil-burner, I'm not okay with more than a 1-2 year plug change interval. Trooper plugs are $2.50 each, and installs are a non-issue.
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Seating
1. Montero's are a 2 in front, 2 in back, 2 in 3rd row, if equipped, rig. I have 3 kids, which means that simply transporting my clan means that I lose my cargo space. The trooper has MUCH more headroom and shoulder room in the front, and in the 2nd row has more than enough room for 3 adults. The cargo area is boxy and cavernous. I've never once regretting not having the factory 3rd row seat.
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2. the 60/40 reclining rear seats in the trooper are very useful for cargo carrying. I think the Montero rear seat is 50/50. might be a wash, but I remember them being more cumbersome.
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Aftermarket
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1. Aftermarket for both is nothing like a jeep or Toyota, but the trooper has locking hubs from warn, lifts from ARB/Calmini/independent4x, and bull bars and snorkels from ARB, too. I have yet to install a snorkel, but it's on my list along with a dust pre-cleaner to make sure my motor is breathing clean.
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2. I didn't find the same type of support for the Montero from ARB when I was looking though other vendors might have popped up to fill those voids.
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3. Parts are readily available for the trooper, and is a blend of Aisin, Isuzu, and Denso/GM parts. Very affordable. My rig has literally needed almost nothing as far as repairs, though I DID make an effort to research the parts I might need like starters, alternators, fuel pumps, bearings, axles etc. Montero parts are not super scarce, but my research resulted in parts that were more likely special order items, and at higher cost. This may just be my area or simply my experience and not the same for other owners.
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Check out these two websites for info:
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http://www.independent4x.com/Isuzu-Store_c_8.html
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http://www.planetisuzoo.com/index.php?sid=3d3a87d038299c425ee8275d57c7e857
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That's about all I have that I can remember that pushed me over towards the Isuzu lineup. I know a bunch of folks at my work who run Amigo's, Rodeo's and troopers and all report the same findings. Comfy, reliable, easy to work on, and a good value if you put minimal regular maintenance.
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I would look around this site at my trooper build thread, as well Montero builds. There's quite a few troubleshooting threads about Montero's where lockers don't work, solonoids have failed, etc, etc.
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The big weak point on the trooper is the oil consumption, and an auto tranny that can be troublesome, though mine is doing fine at 188,000 miles. If you want a 5 speed, the early Troopers are good to go with their 3.2l motors and strong 5speeds.