I've got a third party database that I'm reading from. Now, I know, I shouldn't but I am, so let's leave that asside for the moment. Whatever the trend is out there to design databases void of PKs and FKs hit this vendor because this database is essentially a bunch of flat files contained in SQL Server. So, I knew I'd run into trouble even attempting to bring it into LLBLGen, but I did it anyway. Obviously I'm pretty much stuck because I can't relate any tables. What are your thoughts on allowing us to set the PK outside of the database? Obviously you've thought about it because you decided not to let us manually set it.

You should be able to set the PK in the designer. One requirement to be a PK is that the field is not nullable. That may be what is not allowing you to set the field as a PK.