Welcome Kurt! Thanks for the kind words. Sorry in advance about the lengthy reply.
Rigidity starts to become a problem on Primo builds larger than ~24”. So, it would be recommended that you go with a LR3 for your target size of 48”x36” unless you’re mainly cutting soft material like foam.
There are a couple forum members that have made LR3’s that have a larger than normal Z travel so that will help with the 4” target. But remember you’ll need over 2 x cut depth to account for the cutter length + clearance above the workpiece. You will need more if you have to change bits above the material. Also you are most likely going to have a hard time finding bits that long.
One alternative would be to build a smaller Primo and cut the larger parts in indexed sections. It takes a little more prep, but I have seen a couple guitar necks made this way.
Another option would be to do double sided machining so you won’t need so much Z travel. You’ll have to develop a repeatable process for the flip so the two sides line up but once again I’ve seen that done on multiple occasions.
Now, going back to your original question. My table position is set by 8 leveling blocks located around the perimeter of the center hole.
With the inner table removed, I roughly position the leveling blocks and tighten them in place. I then set the leveling screw (flat socket head cap screw) height by measuring from the top of the screw head to the top of the table around the perimeter. I install the inner table and lightly tighten the locking socket head cap screws. I then install a dial indicator on the router mount and fine tune the table height by taking readings around the table and adjusting the leveling screws and locking screws until I’m happy. Finally, I lock down all the socket head cap screws to fix the table height. It may sound a bit complex but it goes pretty quickly after you do it a couple times.
Here’s an example of using the drop table to work on a pretty tall workpiece just in case you haven’t come across that thread yet.
Let me know if you need further clarification or if you have any other questions. Best of luck in your upcoming build!