Still trying to grok a configuration that will work with my machine. I found I had to adjust some of config.h, a thermistor table in temp.c and check through everything in arduino_168_328p.h . Originally when I thought I had it working around lunch today It turned out I could not get anything with temperatures working. No T: response to reprap host and unable to turn the heater on. I just found the thermistor table before starting to write this and I found a setting for reprap host compatibility which I believe I have set correctly now. The copy of host I've been using is a nightly build 20100713, apparently there was communication protocol change with 20100806. I might have to upgrade soon, which won't be an issue anymore since I have a stepper extruder now.
And after a download of the most recent reprap host release, 20100806, still no response for temperature. Also when I tried to home I found the end stops don't work... crap. I Know that I have inverted endstops, perhaps that's the problem... Oh well I'll get back to it later. I've switched reprap host preferences to use 115200 baud and in my firmware so I don't have to worry about it in the future.
...reading though http://forums.reprap.org/read.php?147,33082 it seems that endstops aren't full implemented yet? and thermistor support was only added recently... thankfully reprap forums have rss, so I can just add this google reader.