I just fitted a 98 Neon trany in my 99 Eclipse about 3 weeks ago....
Here's what was different:
Bellhousing - REquires you to fit your Eclipse bellhousing. Neon uses cable clutch, Eclipse Hydrolic. (Not all Neons use the cable though)
Tranny Mounts - Need to swap over the Eclipse tranny mounts.
Shift Levers - I found thta after installing the eclipse tranny mounts the one shift lever would not move the whole way. It has this big counterbalance on the back.... So I just got out the sawzall..... no more counterbalance.
That wasw about all the diff's. I do notice a diff in the ratios.... 2nd and 3rd seems closer together... 4th seems the same, but 5th gear is way longer.... I would get 25MPH/1000RPM before, now I get 30MPH/1000RPM.
Let me know if you need any more info.
If anyone lives in PA or close, I have a supply of Neon trannys for $200......