What IPA layout do you use? SIL's website has one for Dvorak. You could edit other keyboard layouts with Ukelele or directly as XML.
You could also try adding something like this to private.xml in KeyRemap4MacBook.
<item>
<name>test</name>
<identifier>private.test</identifier>
<inputmode_not>ROMAN</inputmode_not>
<autogen>--KeyToKey-- KeyCode::Q, KeyCode::QUOTE</autogen>
<autogen>--KeyToKey-- KeyCode::W, KeyCode::COMMA</autogen>
<autogen>--KeyToKey-- KeyCode::E, KeyCode::DOT</autogen>
<autogen>--KeyToKey-- KeyCode::R, KeyCode::P</autogen>
<autogen>--KeyToKey-- KeyCode::T, KeyCode::Y</autogen>
<autogen>--KeyToKey-- KeyCode::Y, KeyCode::F</autogen>
<autogen>--KeyToKey-- KeyCode::U, KeyCode::G</autogen>
<autogen>--KeyToKey-- KeyCode::I, KeyCode::C</autogen>
<autogen>--KeyToKey-- KeyCode::O, KeyCode::R</autogen>
<autogen>--KeyToKey-- KeyCode::P, KeyCode::L</autogen>
<autogen>--KeyToKey-- KeyCode::BRACKET_LEFT, KeyCode::SLASH</autogen>
<autogen>--KeyToKey-- KeyCode::BRACKET_RIGHT, KeyCode::EQUAL</autogen>
<autogen>--KeyToKey-- KeyCode::S, KeyCode::O</autogen>
<autogen>--KeyToKey-- KeyCode::D, KeyCode::E</autogen>
<autogen>--KeyToKey-- KeyCode::F, KeyCode::U</autogen>
<autogen>--KeyToKey-- KeyCode::G, KeyCode::I</autogen>
<autogen>--KeyToKey-- KeyCode::H, KeyCode::D</autogen>
<autogen>--KeyToKey-- KeyCode::J, KeyCode::H</autogen>
<autogen>--KeyToKey-- KeyCode::K, KeyCode::T</autogen>
<autogen>--KeyToKey-- KeyCode::L, KeyCode::N</autogen>
<autogen>--KeyToKey-- KeyCode::SEMICOLON, KeyCode::S</autogen>
<autogen>--KeyToKey-- KeyCode::QUOTE, KeyCode::MINUS</autogen>
<autogen>--KeyToKey-- KeyCode::Z, KeyCode::SEMICOLON</autogen>
<autogen>--KeyToKey-- KeyCode::X, KeyCode::Q</autogen>
<autogen>--KeyToKey-- KeyCode::C, KeyCode::J</autogen>
<autogen>--KeyToKey-- KeyCode::V, KeyCode::K</autogen>
<autogen>--KeyToKey-- KeyCode::B, KeyCode::X</autogen>
<autogen>--KeyToKey-- KeyCode::N, KeyCode::B</autogen>
<autogen>--KeyToKey-- KeyCode::COMMA, KeyCode::W</autogen>
<autogen>--KeyToKey-- KeyCode::DOT, KeyCode::V</autogen>
<autogen>--KeyToKey-- KeyCode::SLASH, KeyCode::Z</autogen>
<autogen>--KeyToKey-- KeyCode::MINUS, KeyCode::BRACKET_LEFT</autogen>
<autogen>--KeyToKey-- KeyCode::EQUAL, KeyCode::BRACKET_RIGHT</autogen>
</item>
It's based on remap.qwerty2dvorak in the checkbox.xml in the test folder.
If someone else was looking for a way to change the input method when holding a key, see this question.
Best Answer
Apple has a patent on the autocorrect feature for mobile phones (and possibly for desktops as well). There was a lawsuit over iPhone vs Samsung autocorrect: http://gizmodo.com/5884179/apple-is-now-suing-samsung-over-autocorrect . Moving right along, apple's autocorrect does use keyboard layout to predict a replacement word: http://www.slate.com/articles/technology/technology/2010/07/yes_ill_matty_you.html . Lion will only try this feature if it can recognize the keyboard layout you are using based on a keyboard standard.