Vipers are an extremely exciting thing. When you finally get into a position to start shopping, you can taste it so bad that when you find a Viper that you are interested in (never mind two, as in your case, car lover), it can be very difficult to choose, because when it comes down to it, you just want to have a Viper as soon as possible! But you really just can't let that rush you. You'll end up in trouble that way. Lots of horror stories resulting from being seduced by the Viper. You have to make yourself relax about it so you'll take the proper time to do all the important research so that you don't become a victim.
The Viper forum is a great place to learn just about everything you can think of having to do with Vipers. And all the guys and gals on here are great, being more than willing to answer any and all questions, no matter how many times the same ones get asked. I know this well, since I have been reading for nearly a year, though just a participant as of the end of last year. I am no expert when it comes to Vipers. I don't own a Viper yet. My turn will be next year. Regardless of my Viperless status, I am an avid reader on here, and I participate regularly in discussions, though mostly I am just learning a lot from everyone who has Vipers or experience with Vipers, and so I am constantly taking notes and filing the information away so that I can apply it towards my Viper next year.
Personally, I think that a Viper without its original engine is not a good idea, if resale is important to you. On the other hand, a Viper with a lot of miles on it is not a good idea, if resale is important to you. The bottom line is, if you are concerned with what you will get for it when you sell it, keep looking, because both these 1996 Vipers are not a good idea, again, if resale is a concern. But if resale is not a concern, hell, both Vipers are in the same boat, and so it comes down to personal preference - provided you inspect both, and both come up clean. A Viper with a non-matching-engine number will totally free you in the area of doing after-market modifications. You won't find yourself battling with doing what you want to make the Viper unique because it already has a different engine, so, so what if you do this or that to it? Have fun with it. Make it yours! A Viper that has high mileage will have to have its engine rebuilt sooner than one with low mileage, but then all Vipers eventually reach that stage, right? So, bearing all this in mind, I think it comes down to personal preference. Unless, of course, resale is a concern, in which case, I think you should keep looking, since both Vipers are at a disadvantage. The important thing is that you not rush into this. Another Viper will come along.
Remember to breathe. Don't let the beast ****** you.
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P.S. Another thing that's nice - nay, wonderful! - about the Viper forum is that it's not just a bunch of guys and gals who have nothing better to do than spend time online. It's a place where Viper owners (and even Viper fans who are Viperless) come together, united by the Viper into something closer to a family; a family that really and truly does help each other, including even sticking up for and fighting for each other in times of need. If you've not seen this yet, stick around long enough, you will. I have. It's a grand thing to be a part of something that is more than the sum of its parts. This is the Viper's gift to us. And our gift to the Viper? We keep it alive.
That was touching! I think I may shed a tear! 
