There are no shims shown in the genuine workshop manual, yet on most of the tranny cases Ive stripped/rebuilt(10+) there were shims in them all. More than 1 in most cases, hinting that they are shimmed up at the factory. Ive run them without shims and had no grief tho.
The intermediate shaft does wear, the bearings are usually good but the case hardening on the shaft fails, the bearings do fail after a while, but if its clunking lots, check the hi-lo selector ring on the lower shaft.
On some cases, Ive seen the teeth on the selector ring get mashed up, causing a lot of slop thru the box. Just check the centre splines, and the splines on each gear are looking OK.
One thing worth shimming is the front drive unit. If the clearances open up, the spigot on the gear can end up snapping off. well worth a shim under the gear and a clearance check.
If you need any parts let me know, Ive a few cases and front drive housings spare, but mainly only 413 internals spare(built 3 or 4, 4.16 low ratio boxes now.)