The big bore probably does not want stock jetting, but it doesn't sound like what you have in there is working either. Yes, most likely the jets will be larger than stock by some amount. Use what you have as a baseline, and jet it. There are plenty of good guides around to help you along the way. It's not a guessing game, don't just slap way different jets in it to see how it runs. That's usually a very bad idea...
*edit*
Dave beat me to it. Good post too! I do think the amount of air it can take on should increase more in comparison to the larger amount of fuel it can pull through the jets. IMO larger jets should be needed, but perhaps not as large as one might think.