Andrew: Here is a repeat of Paul Th's diagram, if it didn't come through before.
You ask "Is it too simplistic to say that a higher yard angle simply allows for more sail area behind the mast?". That's not really it. It is simply this - for a given length of mast, all other things being equal, the johanna sail will come out with more sail area than the low balance sail. It is a mistake that some people make with a low balance sail, to think they can haul the sail nearly to the top of the mast. You can't. With low yard angle, you need a a bit more halyard span, or the halyard angle gets too great. I know, I've tried it! Try drawing some pictures of both types, and limit the halyard angle to about ten degrees. You will see. If you want to match the sail area of a johanna sail, with the same chord length, the sjr needs a taller mast.
As an aside, when you make the mast don't be in a hurry to trim it. A bit too long is better than a bit too short, and you can always shorten it later, but its a bit more difficult later to make it longer. How do I know that?
As for your other question: "... if I get the mast slightly in the wrong place, can I compensate by changing the sail plan?"
I am not quite sure if you worded that the way you intended. A different sail plan (ie one with a different amount of balance) would probably affect the helm balance, so yes, you could compensate by changing the sail plan - but that would mean a new sail and possibly new battens - not really an option.
If you mean "... if I get the mast in the wrong place can I compensate by adjusting the the position of the sail" that is something you should discuss with Arne. I believe his sails do allow a little bit of "mast balance" adjustment, ie move the sail just a little bit fore or aft, and that might compensate. A little bit of extra mast height also would allow you to move the sail back a little. But you need to discuss that with Arne.
Another possible option is to rake the mast a little forward or aft. Some people like the look of a forward raking mast on a junk rig, and also the way the sail tends to wing outwards in very light wind, or calm, which is better than having it swing inwards. In choppy conditions, when the wind is light, the sail is said to "sleep" better that way. But raking the mast forward would only reduce weather helm at the expense of more lee helm in your case. Raking the mast aft on a junk rig is rarely done, and I have no idea about that.
In addition, I have read reports that if the sail has fairly long parrels, you can temporarily sling the sail forward a bit or aft a bit, by adjusting a running parrel, in order to balance the helm on certain points of sail. You can get Arne to advise on that too. (This kind of flexibility - mast rake, and adjusting the sling of the sail, are options you don't have with a SJR, so I have never done it).
To continue the discussion, in my humble opinion, I suggest you follow Arne's advice and don't over-think it.
You won't get perfect balance at all times with any rig. On most boats, the best you can achieve is a good compromise, light weather helm is ideal, but too much is tiresome. Helm balance is affected not only by CE/CLR matters, which are a guideline at best. A lot of boats which are about right under normal conditions, develop severe weather helm when sailed at an angle of heel - by all accounts your boat is a bit in that category. Perhaps slight lee helm in very light airs is worth accepting in exchange for a lighter helm in heavy weather.
The amount of balance given to a sail can also affect the helm at times, in the following way: even though the helm is about right when sailing close to the wind - a low balance single sail can cause the boat to become "hard mouthed" (excessive weather helm) when sailing down wind in heavy conditions, simply because nearly all the sail is out one side. This is one of the reasons why some people prefer a higher balance sail, which is less prone to that. A tall, narrow sail is less prone to that, too.
I think Arne has shown you a sail plan, based on his experience, with the mast perhaps a little further forward than ideal, but it keeps the mast clear of the forward cabin and the hatch. A little mizzen sail could compensate for any slight lee helm which might occur on some points of sail, but if you can accept a little bit of lee helm in light airs when going to windward, you might quite possibly find that the mizzen is mostly not a necessity.
(I would consider taking the mast down through that sloping cabin front, or partially - a somewhat more complicated a job in making suitable partners, but that is a matter you would need to assess. An easier hack, which might be rather fun, would be to have an easily demountable mizzen in a socket right next to the rudder post, and plonk a simple little free-standing sailing dingy rig there. You might find you don't need it most of the time, but it might be fun fooling around with in light weather, and the first reef might be to lift it out, roll it up and throw it back in the dinghy. It's in the category of "messing about with boats" if you like that sort of thing.)
Two more thoughts - there is a lot written about modifying rudders for junk rigged boats if you find that helm command is not quite coping with the rig. It is often done. Again, Arne is your go-to person on that subject. The other thought is trim - if you have persistent lee helm you can sometimes cure that to an extent, by altering the trim of the boat a little, ie shifting some weight forward, and getting it a bit more down by the bow.
All of the above are things you can fool around with later, if you are seeking perfection, you don't need to be over-thinking them now or you will never make a decision. My advice is follow the advice of Arne, and get back on the water - be reassured there are plenty of little mods you can apply afterwards, especially with that type of sail. (I am in the same age-class as Slieve - I wouldn't discount his advice either. But I have no doubt a junk rig, even if not perfect, will extend the number of years you can enjoy sailing). But don't let too much thinking interfere with getting it done and getting back on the water. I say that with feeling - it is a mistake I made.)