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I can't exactly remember, but I think the new engine was around $5700. I took my VX to a local shop that I trusted to do the engine swap (not a dealer, Isuzu or otherwise) and they charged me $1,500ish to put the new engine in. Here is the thread where I delivered the sad news about needing a new engine: http://www.vehicross.info/forums/sho...t=22812&page=5
Isuzu has pulled out of the consumer car market in the US so there really aren't any Isuzu dealers left, just dealers that used to sell and service Isuzu's.
As for finding a new 3.5L; that is getting harder and harder to do. When I bought mine I was told that there were only 16 new 3.5L crate motors in the US so I have a feeling that number is way down now if not already at zero.
A few others here have either had their engines rebuilt, installed used engines, or installed refurbished engines and I think most of them haven't had a problem.
Hope that helps some.
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I'd probably got his route if I was going to replace the engine:
http://www.ebay.com/itm/Isuzu-98-02-TROOPER-V6-99-01-VehiCROSS-02-03AXIOM-6VE1-Engine-Long-Block-ILB6VE1-/130954960189?pt=Motors_Car_Truck_Parts_Accessories &fits=Year%3A2001|Make%3AIsuzu|Model%3AVehiCROSS|S ubmodel%3ABase|Engine+-+Liter_Display%3A3.5L&hash=item1e7d861d3d&vxp=mtr
Or something similar with a warranty.