Hi Sal,
I agree with Burkhard in that the correct CG will turn out to be well aft and that the pitch damping should be very high. That said, you may wind up with an airplane that can be managed in spite of some basic pitch instability. You may find that the airplane wants to slowly diverge into a climb or a dive if you don't keep your eye on it, but that it can be managed as long as you stay alert. This is similar to flying an airplane that has a spiral instability in which it will wind up into a left or right spiral if you don't stay on top of it all the time.
Now, with regard to figuring out ahead of time where to put the lead. Rather than trying to come up with the perfect final solution on the first flight, you might consider some temporary expedient for the first flight or two just to learn more about the final CG. I built a Grumman F3F-2 and wasn't sure about CG placement due to the short, fat fuselage and small empennage. In that case, I didn't dare add more lead to the nose "just to be safe" because the airplane could have been out of limits in the forward direction just as easily as out of limits aft. My solution was to temporarily add area to the horizontal and vertical surfaces. I made "gloves" that slipped over the leading and trailing edges of the surfaces to increase the areas by about 40%. The gloves were held in place with masking tape. On the first flight, the plane flew like it was on rails. It recovered easily from a spin and it slowed to a stall with up elevator. Now I knew I was in a safe range. So I removed half of the gloves from the horizontal stab. Flown again, it wasn't quite as solid, but still safe. Then I reduced the horizontal gloves to 1/4 of original size. It still flew OK, safe spin recovery and could make a 3-point landing. Lastly, I removed the final bit of horizontal glove. Still OK. Then I incrementally removed the vertical gloves. In a total of 6 flights, I had safely determined that my GC calculations were correct. The gloves had been nothing more than cheap insurance.
With that huge stabilizer and long fuselage on the llya, I don't think you need to worry about the CG being too far forward. Aft will be your only concern. So you could just temporarily fit a rod to stick out a foot or so ahead of the nose, and put a lead weight on the end of the rod. As a matter of fact, perhaps two rods would be better; one rod on each side of the fuselage or attached to struts. Maybe make the first flight at a CG of 50% MAC. The rods would be ugly and non-scale, but they would allow you to fly safely and learn more about the airplane. Then incrementally reduce the weights as you learn more about the flight characteristics. At that point, you will know EXACTLY where you want the CG and can install ballast in a more scale like fashion if necessary.
By the way, directional stability may be a concern with this model. I see those two little extra verticals and they look like add-ons to me. Perhaps Sikorsky wasn't happy with the directional stability as originally built. Are those extra verticals fixed or movable ? If they are fixed, he was dealing with a stability issue. If movable, then he needed more control.
Dick