Hi Reeves
I am very sad for your part.
My gearbox was rebuild about 3 to 4 years ago.
I wish I could explain to you how much trouble I had.
The main thing that I can say about a gearbox is "if it does'nt give you trouble, leave it alone".
In your case ok. The gearbox was faulty.
My gearbox was removed about 5 to 6 times before it was as it is now.
A gearbox is the most frustating thing I have ever come across.
Even the slightest mm of wear on gears can make it whine it's nuts off. I think this is maybe happening in your case.
You have placed a different gearbox'es gear into your gearbox. The gear's wear do not match and now it is making strange noises.
That is what mine did and they removed it and put it back in using different gear sets all the times as mentioned until it stopped.
I HATE GEARBOXES!!!!

Mine is also having a small sound coming from it when the car is idling.
When I press the clutch in it slows down and stops making the sound.
Sort of a sound when the wheel is jacked up and you spin it around with your ear close to the wheel.
Release bearing it is NOT (in my case).
The clutch was replaced about 8 months ago. (Full clutch kit).
I will replace the gearbox with a 100% remanufactured one when this one dies.
No more struggling taking in and out.
Hope you get it right.
GOOD LUCK.
You are going to need it.