Thanks everyone for the help and suggestions.
The problem has been solved thanks to Chuck Norton and Jack at C.M.C. Engineering. I had sleeves made for the dowel pins holes and used the RobMc pins to align the bellhousing.
This was my first time using the Browell Alignment tool. However, I found that I like the traditional way of aligning the bellhousing over using the Browell alignment tool. To me, the traditional way is more precise. The final numbers are shown below.
