There's nothing really wrong with them.
They have FRM liners, these aren't very good for boost, but aren't really any issue otherwise.
They're long stroke, so don't expect to get more than about 8200rpm out of them.
Crank pulleys wear out and wobble, and will eventually fall off. Mine's been doing it for probably 12,000 miles now.
There's nothing wrong with the boxes either, at least not out of the facelift (01-02) ATRs. The 99-01 ones had 5th gear syncro issues, but if you've got the box out of the car anyway it's not too much extra hassle to replace it. The box itself is quite a hefty unit but, despite common belief, the ratios are fine. They're actually very similar to the S4C ratios, the only significant difference is that 4th gear is quite long.
The myth about the ratios stems from the fact that the H22A7, as fitted in the ATR, has the smallest VTEC powerband of all the Type R engines at just 2200rpm. This makes it easy to drop out of VTEC and has everyone blaming the gearbox, when really a remap would sort it.
Regardless, I think the H2B conversion is a cheaper route to fitting one in a Civic/Integra than getting custom driveshafts and gear linkage made up to fit the U2Q7 box, so you just wouldn't use it anyway.
