The input shaft is shorter than the 4 cylinder input shaft. Also the pilot diameter of the SN95 is much larger than then 2.3 pilot. You can't just toss in a .668 ID pilot bearing, the crankshaft is different--and much smaller than V6 or V8 (94-98 SN95 T5's are all basically the same physically--not counting gear ratios-- regardless of v6 or v8). The bellhousing goes on no problem, just use your 2.3 bellhousing. This is where the easy stuff ends.
You have to have the input shaft ground down to .590" OD. It is not something that just anyone can do either. It's case hardened so you will machine right through the "case" leaving you with softer material. I don't know anyone who's had issues with it but I don't know a lot of people that use V6 T5's on a 2.3 either. I sent my SN V6 input shaft off to Astro and had them properly repair the shaft to work with the 2.3L. It is still a little short but it works; although you don't get quite as much of the input shaft pilot protruding into the pilot bearing. I didn't drive the pilot bearing in quite all the way to help. It's not sticking out or anything it's just not quite fully seated into the crank. Easy enough, and it will never have a problem.
Now the gear ratios are completely different. In the case of a N/A 2.3, overdrive ratio on the V6 trans is higher than a 2.3 transmission, which takes more torque to maintain speed on the highway assuming you keep the same rear end gear. In other words if the rear end stays the same, you will drop RPM on the highway. The 2.3 is gutless as you already know and it may require you to downshift more often if the wind blows or if you are ascending any kind of incline. I run a 3.90 gear in mine (8.8) and highway is about the same as it was with the 3.45/4 cyl T5 .80 overdrive.
The only real benefit is strength and closer gear ratios between the gears. Strength of a 3.97 or 4.03 T5 is not an issue with a N/A 2.3. Even a mild turbo 2.3, the stock T5 will last a long time as long as you aren't just abusive to it. The ratios are the only reason I went to a V6 transmission as I sometimes found that in certain situations the turbo did not like the big split between gears. Also, first gear was so useless with it's 3.97ratio, that it would make zero boost even at full throttle. Then when you shift to 2nd it drops a bunch of RPM and falls on it's face and you have to wait to make boost. Just milliseconds but I'm picky. Still have the old 4 cylinder transmission but it could use synchro's. Ran quite as a church mouse but was getting a little sloppy when shifting.
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