Hmm... a curiousity fer sure!
I am betting that this vehicle started out life as a SJ-410 then received an engine transplant. The factory did not build 410s wirth the 1.3 engine. 410s are 410s because the engine is a 1 liter. That's what the "10" in SJ410 means. It might also be that the Previous Owner liked the badge and stuck it in on the truck.
I am not trying to be a weisenheimer here. What you have posted here just does not add up - and that can be a good starting point for finding and fixing your truck's problems.
One thing that you can do to help clear up this mystery is to find the Vehicle Identification Number (VIN) and run it at the following website:
http://www.decodethis.com/The VIN is typically found on a plate mounted on the side of the dash at the door jamb on the driver's side.
This decoder will tell you once and for all exactly what you have purchased irregardless of what the State Registration Title document (which I assume is what you are referring to) says.
If the filter is new, you are satisfied that the electrical system is properly grounded, there are no injector problems, then it might be a flaky Engine Control Module (ECM).
The first thing that you need to do is to get the part number off the ECM (mounted under the dash by the driver's side door) and get in contact with Surly at the Zuwharrie.com website:
http://bbs.zuwharrie.com/index.php?board=12.0Surly is the ECM God and can probably tell you exactly what year Samurai the ECM came out of and can repair it if you would like. just do a search for "Surly" then send him a Personal Message (PM) describing your situation.
BTW, 2-wheel drive SJs are very rare!
I Hope that this helps!