I would like to ask for one more response which I think requires just a short response. If it requires more explanation, I'm happy to post it as another question.
A: You can leave a tip/bonus, if you choose.
Actually, I have already been paying the FTB annually. This means, that the FTB believes I have been transacting business in California.
A: That's interesting. Then, you really have no reason not to register the corporation, because the annual cost is negligible. ($5.00, I believe).
Even though I have been transacting business in California in the eyes of the FTB, I have not registered with the state.
If I register with the state now, is my failure to register previously any kind of a problem?
A: In theory, you could get a $250 penalty, plus $20 per day for unlawfully transacting intrastate. But, it's not routinely enforced, because the Attorney General or county District Attorney must be involved, and the Secretary of State doesn't refer anything but the most egregious cases for prosecution.
If you're worried about it, then file a final return with the FTB for the foreign corporation, and then form a new corp, either California or Delaware, assign all of your contracts, patents, etc. to the new corporation, and then dissolve the old corporation. Then there will be no nexus between the old corporation and the Secretary of State, so no way to determine that you were ever operating without registration.
Hope this helps.