Yes. The trainspotters (and switched-on scrutineers) can pick the difference from the outside, but the later cartridge forks go straight in to the earlier triple clamps. Brak caliper interchanges, no drama.
The general concencus is that Honda screwed up with the 88 forks - the action is a big step backward from the 87 (and 86) versions of the same forks.
If its only the valving, then its probably an easy fix in 2014. Not sure if they messed with things like bushes and stuff.
Not 100% sure on the axles. Worst case is that you need the axle, spacer and bearings to match the later forks.
Edit: And 43mm from 1983 to 1988 (89 for the CR125). The 86~95 XR250s have 41mm forks and XR650s have 46mm forks, so avoid them. Not sure about 96+ XR250s, XR400s or XR600s - the 600s didn't get cartridge forks until 90 or 91 anyhow.