I must be thick as I can’t see what the problem is then! If that’s how you have the modine plumbed in as said
Pipe from Modine to spigot above water temp sensor & pipe from Modine to the smaller pipe on water pump then it is correct.

All you are doing is bypassing the heater matrix and all the other plumbing should be as ford designed it?

Any more technical questions you will have to wait for another answer I’m afraid as I can’t get the gest to what you mean, of why it’s over heating if your plumbing is as stated.

Another quick search found the below info if any help

https://passionford.com/forum/genera...er-matrix.html