OK, stupid question. I'm sure you have done this, based on your references to files in the original post, but sometimes it gets missed. You did check 'use mods', correct? There's always the chance the last patch or whatever may have toggled this, so it's an easy thing to check.
Also, make sure you back up the appropriate file before replacing anything in the root directory.
As mentioned, you do need to start a new game to see changes ingame, as the save game saves the current state of the .xml files for your scenario when you start that scenario.
Another thing that happens is that if you don't have your tags just perfect (i.e. proper syntax, open and close symbols <>, etc.) the game will ignore any files in between the missing brackets and such, and your change won't take effect (defaults to the original file).
It's easy to accidentally delete a character when you are modding files, and it can be a bear to track them down afterwords. Hence why I practice the 'baby steps' philosophy whenever possible, so that I at least know which change may be hanging me up. Again, it isn't always obvious, but it helps.
Of course, I code in notepad usually, so I don't have an .xml editor to point out issues. In the past, I've had spacing/character issues that have wigged out my .xml using an editor (which effectively damages the file), so I don't use the .xml editor anymore. Railroads was REAALLY sensitive to this, but I don't recall having any major issues in Elemental with spacing, returns and such. Nonetheless, to each their own, and I trust myself more than I trust the .xml editor I have at this point.
And, to verify what BlackRainZ mentioned, some files need to be changed in the root directory, so if all else fails, try replacing the 'root file' after (again for emphasis) backing it up somewhere safe.
Mostly, I'm just emphasizing a lot of what has already been said.
Also, while you didn't mention the coremounts.xml file, the changes you are attempting aren't handled in that file as far as I'm aware. For the benefit of other would be modders, mount bonuses and such are of course usually in the CoreMounts.xml, so that's a good place to start when tweaking bonuses that don't involve production rates.