Just checking- I assume you meant to the internal analog board, to run the CRT?I was hoping to simply connect the motherboard to the internal motherboard
Look, to save you a whole lot of wasted time, energy and frustration, I'm just going to say here: no. Using the internal monitor is not going to happen.
The real killers are the sync/refresh/scan rates. Classic's internal monitors just run at completely different, much lower rates to anything newer.
Moving on ...
OK. This is known as a stealth mod - another useful search term. Stealth meaning from the outside it looks completely original.I do want the original case to be intact / desoldering the ports and add wires so they could match up with the SE ports.
In fact ...
If you plan to use wire port extenders anyway, there's no reason you need to have the motherboard in the same place as in Trash's mod. You can think about other, possibly easier places to mount it, and just make your port extenders longer. Vertically up the left or right side, for example.
This is doubly true if the CRT and AB are removed
One suggestion. Desolder ports from a dead motherboard (like the SE). Use normal external Mac cables for each port. Cut the cables to length, solder the ports to the cut end. Then just plug them in
That way your 6400 board goes unmolested - less risk of killing it soldering, and it can always go back into another case.