AkSys is freely downloadable from Akai's website. When you go to get it just enter an "a" or "*" for the give us your email spam crap they force you through.
You will need an older OS X (or OS 9 if you have a real old Mac around) or a 32bit version of Windows. XP/Vista/Win 7, any of them. But it must be 32-bit because the driver for your USB port on the computer to communicate with the 4000 is only 32 bit.
For 64-bit Windows, Windows Ultimate and emulated XP Mode is the only way to install and run AkSys.
It crashes at times when you load large folders or a lot at once, but it has tons of cool features. If you're accustomed to software you'll notice they thought of some cool stuff considering it was way back in 2002. You can load folders, make PGM's amd set up Keygroup PGM's tweak PGM and FX settings. It's pretty useful if you have the right computer to run it.
BTW- How much RAM is in your 4000? 512MB gets you a decent 31 minutes of sample time.
http://www.akaipro.com/mpc4000/?tt=5Get the 2.00 USB driver unless you have a Win98 PC somewhere (2.01 for that).
And the AkSys installer is right below that.
I played around with the pan control on the REC Gain and now I'm thinking the pot/encoder itself might be part of the issue too. Will have to determine if it's the ins themselves, the encoder and it's board or all of the above. I'm no expert so hopefully other 4000 owners might know something.
Closest I found here was this 2500 thread. But the issue was global in that case not just when in REC mode. -
viewtopic.php?f=21&p=1335838And your last post - YES. It is precisely that.

Again, it's from 2002 so it's a little clunky, but still covers most of what you're looking for.