Don’t do this step. The G400 bootloader as I see it is good, this step just make you more confused.
Now, step by step, one device each time. Let start with UC5550 which is easiest one. First of all, try to update TinyCLR 0.12.0: Gearing up for TinyCLR 1.0 previews
TinyCLR config in this release is much better than 0.6.0 which is very old. By install latest version may solve all your issues, but if you still have more problem, just post.
After UC5550 is good, we will move to next devices. Don’t do anything with Samba which is more complex to you and not related to your problem anyway.