I let the ties that were stained without any pre-stain stay in the press for 2 days after being glued to ensure that any issues with the glue holding would not have anything to do with drying time. When I took the test ties out of the press, it simply took a little twist and the assembly broke apart. Below is a picture of the results after the break.
Note that none of the glue even stuck to the tie but it is practically welded to the unstained oak cross members. So, it is clear that the oil stain is preventing the glue from penetrating into the fiber of the wood.
So, now I need to figure out a way to use the tie that I have already cut and overcome the problem with the glue and stain. So, in my lat ditch effort, I got out painters tape and covered the area that was routed from each tie to fit over the beams. The picture below shows the ties with the tape.
After taping all of the ties I have already cut, I used a brush and painted the stain on the ties with the tape in place and hung them over supports outside to dry. The finish will be rough as I cannot sand this setup and I cannot wipe much stain off of the ties.
I have only cut about 10% of the total ties that I will need, and for all of the rest of the ties, I will cut them to length, then stain, then route the space out for the beam. So, if none of this works, I will route out the remaining middle of the tie and use these whenever the tie must go over a cross member.