It's a big boat and I am not qualified to advise. However, I can help you with some of the maths.
OK, let's take one step at a time. Here is an attempt (without accurate software) to determine the CoE of the original sail plan.
I am ignoring the inner staysail and just looking at the main and genoa. Calculating the geometric centre of each. Calculating that their areas are in the ratio 47:73 (main:genoa) and therefore the CoE is placed at a position of 47/120 or 73/120 on the line marked in green.
I don't have any scale at this stage, but I can see that a vertical line through the centre I have calculated, runs through the clew of the inner staysail on this drawing, or just a little aft of the number 2 port light.

If the drawing is correct (and if my methodology is correct) the CoE of the original sail plan is on a vertical line through the clew of the inner staysail.
Can we agree with that, as a first step?
The next step will be to design a junk sail plan whose geometric centre lies on this vertical green line.
The driving power of this masthead rig (above) seems very much to be in the fore-triangle. David has suggested that a ketch rig would suit this hull better than a schooner. I must say, I can't think of a single advantage of the schooner rig, unless mast placement dictates it, but keeping an open mind, the next step is to look at the accommodation plan, placement of bulkheads, hatches and other structure, and decide what constraints there are on where the masts should be placed.
We could begin by considering the mast placements you have chosen already, and see what sort of two-masted sail plan arises from that.
The chosen rig should be centred around that vertical green line.
Are we in agreement with the first step (above)?
Are we on the right track David? Arne?
(Further investigation of your proposed schooner rig (very, very roughly) I think your geometric centre is about 1/2 m aft of the green line. Try reducing the main and increasing the fore sail just a little).