As appealing as the Pentastar V6 looks at first glance with it's impressive HP and torque numbers, to get those numbers it's by necessity a somewhat peaky engine. This is why we're seeing 5-, 6-, even 8-speed automatic transmissions these days--it's the only way to keep the engine near the "sweet spot" of its narrow power range. Hooked to a 904, I would expect it to be relatively laggy when compared to its intended transmission. I wouldn't think it would be nearly as fuel efficient either. It's a pretty common issue with multivalve engines. No one ever called a Neon a torque monster, particularly with the 3-speed auto. There's just too much port volume to make a broad, flat torque curve as you naturally get with a 2-valve engine like the Magnum V6 or any one of the classic V8 choices. Of course that could be overcome with forced induction, which is why a fairly-small engine like Porsche's flat six in the 911 is an absolute brute, even down low.
If I were considering a naturally-aspirated six cylinder, I'd probably look at either the Slant Six or the 3.9L Magnum. Both are pretty torquey and work well with the low gear counts to which we're accustomed in these cars. Either one is a much simpler swap, too. There are plenty of speed parts out there for both, though an aftermarket 3.9L intake's getting tougher to find--camshafts aren't bad; you can always have yours reground in a performance profile based on a V8 pattern.