"knocking" in 1990 b2600i 4x4

Recently, I've started hearing a knocking sound when idling in neutral. It sounds like it's coming from the area around my transmission. When I depress the clutch pedal, the knocking stops, resuming only when the clutch is released. My first thought was throwout bearing; but I have changed that out, along w/ the rest of the clutch kit, and the knocking sound continues.

I'm not sure if it is connected, but I have also noticed a slightly rougher than usual idle, and slightly decreased gas mileage.

Anyone know what might be going on?

Start checking if its the crank and compression if your last cylinder has no compression or little itll make the crank knock although that has nothing to do with the clutch