I just put a good used transmission in my 99 4runner. To make sure it worked and everything was hooked up right, I started it up without the rear driveshaft put it into gear and with the brake depressed back into park. While going into back into park there is a horrible grinding noise that stops as soon as I let off the brake pedal. Any ideas what this could be? Otherwise it appears fine. Could this be an adjustment of the shift lever harm that connects the shifter in the truck to the transmission under the truck?

 

The rear output shaft is likely turning from internal windage forces. And because it is turning, the parking lock pawl is grinding when you attempt to select park.. There is a near certainty that there's nothing wrong with the tranny. When the driveshaft is installed and the tranny put into park with the truck motionless, my money says that there will be no 'grinding'.

 

I just put two and two together when I noticed the shaft was still spinning in neutral. Thank you so much for your help!!

 

You got it figured out.
As millball says grinding should go away with driveshaft installed.

Brake won't do much without driveshaft.