Rebuilt 5-speed making noise

[Xoloski]

Hi all,
I am Steve AKA Xoloski, from southeast AZ and this is about my 1993 Sidekick JX. 
The trans was whining and I didn't want a used unknown quality transmission so, I instead bought a good kit with Japanese bearings and seals. The syncros were good so I didn't buy them.
 
Also installed shifter sheets & shift lever socket. Installed new LUK clutch, pressure plate, throw-out bearing, and pilot bearing. 
I had the flywheel turned at my local and trusted machine shop. New transfer case seals and I replaced the transmission mounts for good measure. 

I pulled the trans, separated the transfer, split the cases, and replaced all 7 bearings, and all seals. 
Everything went smoothly and there were no extra parts upon completion. The only issue I had was transmission reinstallation because the top right dowel was a wee bit distorted and didn't want to engage. I slightly chamfered the trans case and it went right together with all engine to trans bolts going in by finger, then torqued to spec.

After reinstallation, new proper lubes, and cable adjustment, the transmission still makes a whining noise in neutral, clutch released, transfer in neutral. The noise goes away with clutch depressed. The noise is not related to the throughout bearing. The noise is present driving in all gears, though less noticeable in 4th, as would be expected. Please see videos, and yes I know my idle is high but, that is a separate issue.

I did buy and install a new Allstate input shaft as the journal that mates with the pilot bearing was excessively worn. The shaft measured exactly what the OE shaft did. The needle bearing between the input shaft and the main shaft looked good when removed although there was a slight wear on the ID bearing surface of the input shaft but no visible wear on the OD of the main shaft where the needle bearing rides. Actually, all the removed bearings looked serviceable without excessive wear. It was obvious that I was not the first to open the cases. The countershaft middle bearing was more of a roller bearing than the supplied ball bearing, but the diameters were right and everything pressed off and on properly. 

The only things I can think of causing the noise would be:
1) the new input shaft gear does not mate properly with the OE countershaft gear because of countershaft wear. (which may go away with time as the gears lap)
2) there is damage or lifetime wear to the countershaft, even though the input to counter shaft lash in unnoticeable.

Please tell me what you think... https://photos.app.goo.gl/RzyBFySpq1DozYxv7