Transfer chain not fitting low range gears from Trail Gear kit

Finished and closed the transfer, mounted, but testing it is awful until now, very noisy sometimes. Especially when starting 1st gear or reversing. 

What kind of noise, reduction gears are notorious for a lot more whining.

I completely agree with Lambert 
I have sj box with trailgear gears reverse and 1st are very whining 
I just change oil regularly 

There is an awful whine and grind the frist 1000km then gradually less but never goes away completely. I would change the Oil before 1000km and then before 5000. And it Will look terrible with metal powder and shavings.
This comes from the new gears that is not profile ground to shape and must be run in. Terrible but normal.

Also your New gears are at less helix angle to take more ratio without adding too much thrust force inside the gearbox wich add noise. 
With less angled teeth there is less overlap from one tooth to the next making more noise. 

Will get better. After running in.