Someone else is gonna have to answer the skill questions cause I know exactly nothing about that.
Though one thing I think is wrong about the guide is creating the *.lsb file outside of the editor. I'm pretty sure you can (and should) do that inside the editor using the resource manager.
On to the part I do know something about. So for your #2 problem this is related to creating an lsb in the resource manager that I just mentioned. I'm away from my editor at the moment so I can't make fancy screen shots for you but hopefully you'll be able to find the buttons. This is an image from another tutorial of mine that is pretty close:
http://i335.photobucket.com/albums/m468/SniperHF/StateMangerTutorial/Create%20Package.pngTo make a new template, first you must use the resource manager and add a package to your mod. You can put it in the folder you described. In the resource manager on the top left is that button.
Then once you have the package created go into the root templates window and add a a template to that package. I believe the "select LSB" thing is #4 on the screen? That's unnecessary. You do need to pick the filepath though under "properties". Point that toward the package you created before in the resource manager.
If you still can't get it I can make a proper tutorial once I have access to my editor again.
For #3.
You shouldn't need to remove entries from the XLSM files. The only way the XLSM files would overwrite changes from patches is if you were using old XLSM files. I just add new lines at the end of each file for my stuff. Or where appropriate under the different headings. Also make sure you have the stats folder in the right location.
#4 and #5. - Testing and getting the mod to work.
So if you want to add all the skills back to main, did you make your mod main dependent? If so then your mod should have all the levels and scripting for the campaign.
All you need to do is publish it which you can do from the top menu, you don't need to move any folders. Once you do that it will automatically create a .pak file in your mods folder under Documents\Larian Studios\.... But this is not necessary for testing, it's only necessary when/if you need to distribute your mod to other people. Your mod will be visible in the mod list just by having created it in the editor.
Also having that .pak file present in your mods folder will cause your mod to be read-only until you remove it. So again, only do that once you are ready to distribute it and then remove the .pak file from the folder so you can go back to making changes.
Far as the nuts and bolts of testing, my suggestion would be to create your own test level within your main dependent mod. Just add new level, add a terrain, an AI seeder, 2 start points. Generate the AI grid. And there you go. Then you can place enemies and copies of your skill book and even test vendors to make sure your stuff shows up.
