Despite the fact that I said that I saw no immediate need to upgrade to Windows Mobile 6.1, one of my friends convinced me that I needed to try it out. So far I haven't really seen a difference except for layout and UI, it might be a bit faster, but not exceedingly so. I installed the Kavana 6.1 ROM. Setup was fairly simple, just follow the prompts. Once finished I noticed incorrect key mappings for some keys and so I installed the eT9 language pack linked on the download above. This fixed a majority of the problems but there were still problems with alt keys.
I read through some tutorials and thought I was going to have to write my own keyboard layout file and registry entries to use, this turned out not to be the case, thank goodness. I was poking around the directories (initially the Windows directory) but found what I was looking for in \Program Files\eT9\. Here are all the files that the eT9 install installed and fixing my problem was as easy as editing the eT9.Excalibur.0409.kmap.txt file (409 is the ID for English). The structure of these files are really simple provided no one messed up really badly and wrote the wrong hex for the keys, that would be less fun to track down. I've posted the fixed eT9.Excalibur.0409.kmap.txt file.
I'm assuming what I have is a standard US layout, so if you're having problems with the English layout for the eT9 pack, download this file and just drop it in \Program files\eT9, do a restart and hopefully all will be well.
Note: For some reason Drupal decided that it needed to rename the file eT9.Excalibur.0409.kmap_.txt, take out the extra underscore when you download.