here are a few links for kana training
http://www9.big.or.jp/~mshinoda/
http://www.parara.com/type/index.htm
Here are a few that are independent of layout
http://members.jcom.home.ne.jp/gangas2/download.html
http://www.kentei.ne.jp/key/downroad.html
http://www.vector.co.jp/soft/win95/edu/se236568.html
As a user of an alternative layout, namely colemak, you may be interested to know that there are actually an extremly large number of alternate key layouts for Japenese input as well. Although qwerty romaji and JIS kana are the defacto layouts (a legacy of technologically poorer times and wapro machines), neither are actually very efficient for Japanese, unsurprisingly enough.
Here is a big list: http://jisx6004.client.jp/layout.html
try some out in your browser: http://kirinsystem.net/diary/?date=20060403#p01
Personally, the romaji style layouts fit my style best, as they neither require 4 rows of keys nor excessive shifting, while often containing shortcuts for things such as ん, "sutegana" like ぁぇぃ, っ, as well as "youon" like きゃみょ
Current front runners for me are Yatsugashira and Kyuuri-kai, both of the "yamato-narabe" style.