You should not have much difficulty with pilot jets and idle settings, or getting the main jets right. The main difficulty is usually with the needles and needle jets. A Mk2 Amal is very similasr to a VM MIkuni of the same size, and the Mikuni needle jets and needles will fit the Amal carb. If you start with the 0.106 needle jets, you should be able to induce a miss by lowering the needles, then raise them until the miss disappears. If you are slightly too rich on the needles, the motor will be sluggish, but the bike will still perform OK. To get best performance, try using slower taper needles If you put Mikuni and Amal needles side by side, you can see where the taper begins. The needles in almost all carbs are the same diameter at the parallel part. The differences are in the rate of taper. Where the taper begins depends on the size of the carb.
If your motor always performs better in cold weather, you can probably use slower taper needles, and it will be better at other times.
The rate of taper depends on how the bike is to be used and the size of the inlet ports. A MX bike will use quicker taper needles than a road race bike, because you use the throttle in a different way.
It is a choice between two things. If you open the throttle fast with quick taper needles, the response is a mixture which richens quicker but you have more air. If you open it slow with slow taper needles the mixture stays leaner, but you have to feed the throttle on. The latter situation gives better performance.
Mikuni needles and needle jets give better performance in Mk2 Amals. But if I was in your shoes, I would buy a few 0.106 Amal Needle jets and drill them using a combination of metric and number drills, to get the intermediate sizes in between 0.106 and 0.107 inch. When I do it, I use a hand drill and only take one slow cut to increase the jet size. You need to convert between metric and inch.
Normal carbs are at their limit with petrol. Fuel injection and a programmable ignition system would probably be much better.
When you jet for petrol, it is twice as critical as when you jet for methanol. With my carbs using methanol, the difference in needle jet size between fast and slow is half a thou of an inch. For you using petrol, it will be half that.
When you raise and lower the needles, you change the internal diameter of the jet in steps of one-fifth of any increase you have made by drilling. The correct position of the needles is one notch away from the miss, when you ride the bike. When you get it right, it makes a big difference. Normally when you ride a bike, you do not suspect when it can be faster, until it becomes faster. It is the same with raising and lowering the overall gearing. You do not know what will happen until you try it. A torque increase only becomes evident when you raise the gearing.
The Commando engine is strange - the motor always tends to spin up at the same rate regardless of the gearing. Lowering the gearing does not usually give better acceleration, as it does with most other bikes.