I have fixed the problem with combined iMessages and I still only use a single apple ID account. Before everyone points out that you are not supposed to do that, I know. I have weighed the costs of not sharing and I am comfortable with my decision, it may not be correct, but it works for me.
My "fix" has been working now for more than 15 days. I will run through exactly what I did, and in what order I did it.
The products I have are:
2011 Macbook Pro (High Sierra) FaceTime associated with email #2, iMessage WAS linked to my phone number (more on that later)
iPhone 6 (mine, iOS 12) iMessage and FaceTime associated only with phone number.
iphone SE (wife, iOS 12) iMessage and FaceTime associated only with phone number.
Iphone 5S (daughter, iOS12) iMessage and FaceTime associated only with phone number.
Old iPad (3rd generation iOS 9.3.5) iMessage and FaceTime associated only with email #1.
Previously on this thread I mentioned that I was going to roll back to iOS 11, but Apple is no longer signing that version so this is how I got everything to work.
1. I signed out of my apple ID on every iOS device and turned off find my iPhone. I deleted all of the iMessages from every contact that shares the single apple ID, on every device.
2. I signed out of my apple ID on my Mac and then turned off iMessage all together. I then deleted all messages.
3. I factory reset my iPhone and restored it from backup. When setting it back up I only allowed my phone number to be associated with my iMessage and FaceTime. (I do not use iCloud photos on any device, but I do use my photo stream. All of my devices are backed up up every night to iCloud. Additionally, AirDrop and handoff is disabled on all iOS and Mac devices)
4. I factory reset my wife iPhone and restored it from backup. When setting it back up I only allowed her phone number to be associated with her iMessage and FaceTime.
5. I factory reset my daughters iPhone and restored it from backup. When setting it back up I only allowed her phone number to be associated with her iMessage and FaceTime.
6. I re-signed into my apple ID on the iPad and I only allowed email #1 to be associated with its iMessage and FaceTime.
7. I DID NOT activate iMessages on the Mac. I have read in other forums that this can cause the combining of iMessages again. I am not happy to no longer have iMessages on my Mac but it is a sacrifice I can live with.
I have subsequently updated all iPhones to 12.0.1 and they have still not combined a single iMessage.
Prior to this fix I was also getting wrong iMessages from my brother who shares a single apple ID with his family. This problem has also been remedied with this "fix".
I understand that this may not be THE way but it is A way, and it has worked for me. I will provide an update if this workaround no longer works with further iOS updates.
Thanks