You will want to take it off the trailer and get it as low to the ground as possible. Make sure you can leave it in this position for the amount of time it will take you to get the structure back into the boat. You will notice once you get it blocked up, and take the stringers out the boat will flex underfoot.
I used a 6x6 landscape tie under the stern area where the transom meets the keel on my boat. The lower you can get it, the easier it will be to get materials/people in and out of the boat. I used short screw jacks and blocks to adjust the boat side to side /corner to corner making constant measurements in an X pattern so the boat didnt turn into a potato chip shape. Without a transom core and a deck fiberglass boats turn into a Jello mold.
Here is what it looked like after I poped the center stringer out, I had plenty of poor repairs and installs in the hull to fix.
I ground it down smooth, dried it out and then stuck my center stringer down with putty, and made nice smooth fillets along the sides. This is actually the raised portion for the tank support, but I used the same paint sticks to support the stringer while the putty setup. You get the idea.
