Alright the things I would do if I was that far into it:
Clutch - All you need here is a stage one or maybe stage 2 from any of the respective brands. I have used SPEC, but RAM and Exedy are great. I have heard people have good experience with the Zoom (I believe this is an OEM replacement from parts store) and generally most clutches are good for at least a few mods.
Flywheel - If you have time on your side, you could just get this resurfaced at a machine shop for say $10 or so. If that is not an option, you could look into upgrading to an aluminum one to shave some weight, or just stick to OEM ford.
I would go with ARP for the flywheel and clutch bolts
Throw out bearing needs to be a motorcraft part. Some people do get lucky with aftermarket, but that is few and far between.
The pivot joint/arm should be replaced. Mine fell apart around 200 miles after doing a clutch. Terrible feeling when you look down and seeing the fork sitting below the dust shield.
Pilot bearing should be replaced, I would stick with OEM ford here as well, though it doesn't get the bad reputation like the throwout bearing from aftermarket sources. To replace this, hammer bread into your input shaft until it pushes out. Usually takes about 6 pieces of merita.
I would throw away/return the clutch cable you bought. I had the steeda one and it snapped in about 2 weeks. Replaced with OEM ford and never had an issue. If I were to do it all again, I would just buy the whole kit from Maximum Motorsports.
Input shaft should not need replacing.
And as Lutter said, I would do the rear main seal since you are that far into it. Be careful when doing this, a lot of people screw it up then just have to go back into it again in a couple weeks time.
It's a clutch job, don't overthink it