American and Chinese versions, actually, not Japanese.
As far as the clipping, you can definitely clip pretty much any piece of audio gear if you run overly hot levels through it. You're possibly clipping the inputs, even before it gets to the limiter. Or maybe just sending it too much signal for the limiter to handle. You say you haven't setup the gain staging properly yet, so I don't understand how you can know whether there is a clipping problem until you've calibrated your audio path properly. Back off the volume until it stops clipping and then use the gain makeup.
The other thing is, you probably should swap out the tubes for new tubes. If it was bought NOS, then it has been sitting unused on that store shelf for eight years or more. My USA made PRO VLA was built in 1999, and I'm not sure when production shifted to China. So your unit could easily have been in that box since the mid 90's. The tubes could have a leak or other problem, so replacing them would be the first thing I'd do.
The US and Chinese versions sound different, not necessarily better or worse depending on your application. I've owned both.
The older USA version pumps easier and has a slightly less refined sound. The new Chinese made version is cleaner with a smoother compressor action, more like a mastering type compressor. In other words, the USA version has more of a "sound". It's subtle, but that's the best way I can describe the differences I've heard. I don't like one more than the other, they are just slightly different.
I experimented with replacing tubes in both units. Tubes that I liked in the USA version I didn't like in the Chinese version, and vice versa. This is why I think any discussion about replacing tubes in the VLA has to also include information on which version is being modded. To just throw out tube suggestions without indicating which model is not really helpful because they do sound and respond differently.
Because the Chinese version is cleaner and smoother, I found I liked to put more colored tubes in it, to give it a little more personality. Those same tubes did not sound good in the USA version, which needs cleaner tubes to get the most out of it in my opinion. The variations are endless of course, and it is possible that one set of tubes would improve both. I certainly didn't test every tube out there.
But unlike some people, I did notice that swapping tubes makes a big difference with the PRO VLA. Theoretically it shouldn't perhaps, but it does.
The older USA version has Allen nuts on the front of the unit as opposed to the flush fitting Phillips screws on the Chinese version, and the top lid of the case on the older unit has a couple notches taken out on the front left and right sides. Otherwise they look the same.