Hope I can help some here...
What is the intended use of the car? mostly street, mostly road course, or an even split of both?
Shock mounts:
I would stick with stock for the upper mount. The BMW mounts are bump rubber elastomer material. They are actually quite good. Urethane is a horrible component for suspension material. That's a story for another day. The lower shock mount is the abomination. I am in the middle of designing something better but I'm sure someone sells an articulating bearing version which is what I recommend. However, you are already planning to swap the rear lower control arm (good move) so this doesn't apply.
Rear Spindle Ball joint:
This is already a ball joint from the factory with a nice dust boot. It is NOT a bushing. Not much gain there switching to a spherical bearing.
Rear Trailing Arm Set:
Like
@ShocknAwe said... this has no benefit. The factory arm is more than adequate and is designed to bend in the case of an accident and not puncture the gas tank.
Camber Plates:
I definitely recommend the Vorshlag camber plates.
Toe Arm:
Definitely go with the Rogue toe arms. The M3 version will not work but I think you already noted that.
Upper Wishbone, Guide Arm:
As for the upper wishbone and guide arm, this depends on the intended use of the car. The Rogue ones are good if you need the adjustment. If you don't need more than factory camber the OEM M3 arms are a good choice.
Random Note:
Maybe I'm misunderstanding what people mean but this is meant for the e46, not the E9X
https://www.ecstuning.com/b-genuine-bmw-parts/rear-control-arm-right/33326781626/
Basically, the E90 rear suspension is very complicated, too much to really cover here but I'll make a few notes... Suspension geometry plays a huge role on how the car feels under load (acceleration, braking, cornering). The Non M suspension is meant to have certain toe settings under certain conditions, hence all the rubber bushings. It was actually designed to be neutral in cornering and then understeer when at the limit. Below is the toe curve of the rear suspension where red is static, blue is cornering and green is braking. Unfortunately, I don't know what is is under acceleration which is what most people complain about. I'm in the middle of trying to figure it out plus many other geometry differences in detail (winter project)
View attachment 17129
When you go and change things you change these curves. Not saying its a bad thing just making a point. Its also worth noting that simply putting the m3 arms (lower control arm, wishbone and guide arm) doesn't get you the M3 suspension. The rear spindle has different pickup points than the non M. The rear subframe has different pickup points for the toe arm (hence why the M3 arm is longer) and the rear lower trailing arm (Anti dive). Another note... if you replace every rubber bushing with a ball joint the rear suspension (M or Non M) will be locked into place. If you do get it to move its because an arm is bending.
Anyways, back to the point, once you do all of the items in the rear it may take a while to find a static toe setting that will then work when the suspension is loaded based on your wheels, tires, shocks, ride height, etc. The factory toe settings for the M and Non M will not apply. Someone correct me if I'm wrong but total toe in the rear of an M3 should be 10' and Non M 18'. I'd start with 13' (.21 degrees) total toe in rear and go from there.