Yes, the rule of thumb these days seems to be to have the midpoint of the boom and battens of a junk rig matched to the CE of the original bermudan rig. ie to assume that the CE of both rigs will coincide on tha same vertical line. That puts your current proposed mast position about right, to a few inches, for a 33% balance sail, I would say, though you should draw it accurately and get a second opinion.
Here is a little spiel on mast height.
For a normal junk rig with soft batten parrels (that means currently nearly all junk rigs) there are some additional horizontal forces necessary on the sail and battens, to keep the rig from swinging forward. This is why other extra running and standing parrels are often added, to keep the sail draping nicely without severe creases etc. If there is a harmony between the mast-balance and the yard angle, on most junk sails, these forces are kept to a minimum. As a general rule, we can say that high yard-angle goes best with low mast-balance, and low yard-angle is in harmony with high balance. This is one reason why the Amiina SJR has a relatively low yard angle. The sail is very well designed and harmonised, and horizontal forces on this sail are quite low, and pretty much taken care of by the running parrel downhauls (a feature of that particular design) - no other parrels being necessary (at least on my little boat).
Paul Th has an excellent diagram which demonstrates the relationship between yard angle and mast balance (which assumes a fixed mast height and a fixed halyard sling point close to the centre of the yard).
Arne has analysed the problem in another way, by considering the angle between the halyard and the mast when the sail is fully hoisted. (He refers to it as “halyard angle”). The halyard is normally attached to about the midpoint of the yard. The lower the halyard angle, the more vertically it pulls and the less are the horizontal forces required to counteract the halyard’s forward pull, to make the sail drape nicely – a better behaved rig. A correct relationship between yard angle and mast-balance amounts to the smallest halyard angle, for a given mast height.
Properly designed, a low balance/high yard-angle sail does not need to have a mast as high as the peak of the sail, as you will see in all of Arne’s drawings,
Another way of reducing halyard angle is just to increase the height of the mast, but that can mean using one fault to overcome another.
However, there is another reason why the mast must have sufficient height. Even though the halyard angle is kept to a minimum, when the sail is hoisted to its highest, the halyard still has some angle away from the mast, which means that it has a horizontal component which does not help, and a vertical component which is less than the pull on the halyard. What this means is, if the halyard angle is too high, the effort involved in hoisting the last metre or so of the sail becomes quite great.
In the case of a SJR sail, that means two constraints. For the Amiina planform, with its low yard angle, the mast height must not be lower than the peak of the yard, in fact a little higher is desirable. The other constraint is that the Amiina sail is designed for and works well with running parrel-downhauls. But these lines are spanned so that each span controls two battens. The lowest batten (be it the boom, or some other batten when the sail is reefed), must be sufficiently clear of the deck if there is to be enough room for the span. If the mast is stepped forward of a cabin top, this presents little trouble. But if the mast is standing on a flush deck or over a deckhouse, then the height of the boom above the turning block for the parrel downhaul (ie the deck) must be at least just a little more than 50% of the distance between battens. That is a further constraint on the height of the mast, for a given sail area. You need to think about these things when designing a SJR – minimum height of boom above the parrel-downhaul turning blocks, and minimum height of masthead.
You can make some scale drawings and you will find that for a given height of mast, a low balance sail can be made to have a little more sail area than a high balance SJR. Or, conversely, for a given sail area, the SJR will require a slightly taller mast.
Here is another "eyeball" comparison, but you can see where the mast height is, in relation to the original bermudan mast height, and compare in each of these two sails
The SJR is a powerful sail and Slieve will advise (correctly I think) that there is no reason to pursue an excessively large sail area. Also, within reason, a slightly taller mast is not such a disadvantage as may appear (apart from a bit of extra windage when the sail is reefed.) The height of the centre of gravity of the mast, sail and battens is not increased all that much by a bit of extra topmast, and the effect on initial stability is next to zero. When the boat is heeled to a great angle, then the taller mast will start to show some effect on righting moment. Then you will be glad you have a junk rig anyway, because it is so easy to reef.
You just need to do some drawings and do some calculations to see that we are not talking about a serious disadvantage. Unless the boat happens to be very tender under its original sail area, then it is just one of those things we tend to over-think. I hadn’t thought about that when I made the rough sketch, and didn’t really consider sail area, it was just eyeball. When drawn properly to scale, a SJR rig with a comparable sail area usually comes out with a mast about the same height as the original Bermudan mast, and a Johanna type, of moderate aspect ratio, usually comes out with a mast a bit less than the original Bermudan mast. If you are worried about it, you might like to consider a hybrid mast, with the top, say 25 – 30% made from carbon fibre. In practice I have not heard of any SJR which suffers from too high a mast (though I know of one or two which have masts a bit too short).
Obviously, everything within reason. These are just things to think about, and maybe to discuss with people like Slieve or Arne, and there are others, who have a wealth of practical experience.