Bumpsteer is a very complicated thing to set. You need a bumpsteer gauge to do it correctly. You've come this far, so, ya, just leave it level with the A arms.
When you have free time, go to youtube and search for "Setting Bumpsteer" Its WAY more complicated than most people know.
I have never ever lost any ps fluid while doing any of the tasks you have. That would concern me. Keep a Very close eye on that. Maybe pull the flexible boots back, and see whats going on.
Those spacers look like the ones that come in the Max. Motorsports CC kit. I would just put them aside for now.
No, I'm pretty sure the long one does not go on the top, threaded part of the shock spindle.
The funny looking rubber bushings is the bump stop. it points downward.
It goes inside the dust boot. It goes right at the top, again, ponting down. You use a zip tie around the top. where the groove is. The CC plate kit comes with the same bump stops. I would use the new ones from MM.
Your bet is to go to the web site of the brand shocks you got, KYB? what ever brand, and it will give you installation instructions.
Also, check out the MM site for instructions, they have everything there.
Installation Instructions : Maximum Motorsports, the Latemodel Mustang Performance Suspension Leader!
Correct on the springs and iso's. Get the iso's on as far as you can, a little wd40 might help. If I recall, there is a little notch in the A arm, where end of the spring bumps up to. That would be the correct location. Not 100% on that, but otherwise, yes, as close to original position as you can.
Then, straight to an alignment shop.