So everything went well and I was able to harvest seeds from all the crosses I made as well as getting some seeds from using a Silver Nitrate & Sodium Thiosulfate solution on a clone to make pollen to pollinate the mother of the Master Kush/Chocolope cross that I made years ago. I gave a friend of mine a clone years ago and he's been growing it ever since. He had to stop growing for awhile and didn't want to lose the strain so I got a clone from him, grew it out, made a couple clones, and then used one to make pollen with the silver nitrate method and pollinated the mother. We have yet to see how close plants from the seed are to the mother.
There are a few things I noticed. I'm convinced that despite only pollinating a branch or two that it reduces the yield across the entire plant when you produce seeds. Not significantly but enough to notice. I grew two Strawberry Kush plants. Both were different pheno's with one being much more larger and robust. I pollinated a branch on the big one which was about 25 - 30% larger than the other one when I started them in the flower cycle. The smaller one ended up producing more than the larger one. It's not scientific but I am convinced that seed production effects the entire plant and not just a single branch that was pollinated. It makes sense though because the plant's goal is to reproduce so it is going to be sending as much resources into seed production as possible.
Anyway I'm happy overall with this project. I learned quite a bit along the way.