The bone nuts should be fine. I normally buy mine from UK eBay or Amazon sellers because it's not much more in actual outlay (though % wise it's a big jump) and they arrive sooner.
Straight shaft pots normally come in two sizes, 6mm or 1/4"(6.25mm) and need a knob with a grub screw to stop the knob from slipping. Splined shaft diameters are measured on the outside of the splines, so you will probably still have issues with the new pots as the internal splines on the knob will have a less than 6mm diameter.
You can of course, gently squeeze the two sides of the splined pots together, which will help get the knob started on the shaft, but it may end up sitting high on the shaft as the splined section will remain the same diameter at its base.
I'd be tempted to try and count the number of splines on the inside of the knob. If it has 18, then you need a coarse spline split-shaft pot. Use a marker pen to mark each spline as it's counted to avoid confusion. This seems the most likely cause of the knob not fitting as the splines on the shaft won't fit properly into the splines of the knob.
Once you've got some finish on the headstock, that will reduce the tuner hole diameter slightly (so allow the finish to go over the edge of the tuner holes) and will make a tighter fit for the bushings, so I'd wait until you've got the headstock all finished before worrying about the bushings.
You are certainly going to need to do something with that nut. On a zero-fret guitar, the nut is only there to stop the strings moving sideways as the strings should rest on the nut. At the moment the slots are far too shallow and won't allow the strings to rest on the zero fret.
You are going to need to remove the nut and cut the new nut off the guitar, as the zero-fret will get in the way if you try to deepen the slots in situ. The nut will be quite fragile as the slots will be deeper than on a normal guitar, so that base section will be thinner and weaker as a result. You don't want a lot of excess height on the nut, as the 'teeth' on the outside of the low and high E strings are then likely to catch on something (clothing etc.) and snap off. The higher the 'teeth', the more leverage there is on the base of the nut and the more likely it is to snap at the base of the E string slot.
You'll need to deepen any pre-cut nut slots, then file down the base of the nut so that the string can run between the 'teeth', but not rest on the bottom of the string slot as it runs back from the zero fret to the tuner. You want the height of the teeth such that the top of the string is level with the top of the nut. Also, round off the edges of the nut, so that a) it doesn't hurt your hand and b) it is less likely to catch on anything and snap.
I'd be tempted to make the nut slot deeper using some needle files. It looks like it's been cut on a bit of an angle, so it's deeper on the top E side than the bottom E side. A deeper slot means you end up with a bit more meat in the the base of the nut, making it stronger.
I am a fellow Ramones fan. Saw them twice; Hammersmith Odeon in 1978 (probably on the Rocket to Russia tour) and 1980 at Exeter University on the End of the Century tour.