For the Rear arms (bushings that are located in the rearend) I like to take a small drill bit and drill a series of holes in the bshing and it will eventually come out. Clean the metal sleeve up very good with a wire brush then install the new Poly bushings.
Maximum Motorsports sells a nice tool to install the bushings, but I have always used a deadblow hammer with good success.
Pinion Nut has nothing to do with the rear arms...
To check the pinion nut you remove the driveshaft and if the rear end flange wobbles around then you have an issue, but it isn't as easy as retorquing. When the pinon nut is torqued to spec it crushes a crush sleeve, if you torque it to far you will have issues and the sleeve will need to be replaced, then the rear has to come apart.
You want to make sure you use loctite on the bolts and antiseize as well on the bolts where they will sit inside the sleeves. I have the TQ specs at home but you also want to TQ them into place and make sure the arms still articulates smooth.
Perfect time to re-enforce the TQ boxes while it is all apart. I make a kit if your interested.... PM me.