Using the rim of the wheels should be enough for initial alignment. I would not machine anything away from the wheels - you might find they are hardened, and machining material away will upset the balance. Also drilling the crankpin for keys is not a good idea - it could lead to stress cracking in the wheels and besides, the crankpin is really hard and won't drill. Final alignment is done using a lead or copper hammer - sounds brutal but this is how it is done.
Best would be to find a shop that is familiar with pressed-up cranks. They have the experience and tooling, and a single-cylinder crank like yours should be pretty simple for them to do. If you try it yourself you will need a really good press, about 20 tons minimum for a crank that size and one that doesn't squirm or distort as it is loaded. Distortion in the press can lead to the pin going in crooked which can lead to a wobbly crank and in worst case can irreversibly distort the hole in a wheel. And you will need to develop a feel of how to knock the wheels about for the final alignment after they are pressed together - this takes a while. Best to start with about a 5 pound copper faced hammer, and start with light taps.
If you have trouble sourcing a rod kit, try Alpha Bearings.
Heck, they can probably recondition your old rod if you can't find another, and fit you up with mating pin and needles.
a couple of additions:
Another reason for a rigid press is it helps, when adjusting the side clearance on assembly, that the press doesn't "wind up" and jump all at once, and overshoot your side clearance. Then you have the problem of having to slightly separate the wheels on the pin.
Also, it would be good to know if you have a stepped crank pin - one that is larger where it fits through the rod than it is through the wheels. This is uncommon, and very unlikely in your case. If you do have a stepped pin, you will need to make up a bolster that supports one wheel and lets you press the pin, with other wheel still on it, out of the supported wheel.
If you do overshoot when setting the side clearance, you will have to resort to such a bolster anyway, so it might be a good idea going in to have at least an idea of how you could make a bolster.