Jenny,
You are asking two separate questions.
1. On the ILR: No, I don't believe you'll be able to apply for ILR until your spousal visa two year period is (nearly) up. Check with an immigration advisor, but I have heard that the problem is that when you switch categories, the Home Office zeroes you out and you start over in terms of accumulating your time toward ILR. Since you switched from a work permit holder to spousal visa, I expect they will not consider the work permit time towards ILR. I have heard they have a general policy of discouraging category switching.
2. On citizenship: I know (because it was what was done in my own case) that it is sometimes possible for the Home Office to waive certain criteria on a citizenship application if you want to try to get it a little earlier. I had not had my ILR for an entire year when my naturalisation application went in. Since you had significant work permit time before your spousal visa, it may be possible in your case to ask them to exercise discretion in your favour. It's worth asking a solicitor!
I think in order to get them to do so, it would pay to go to an immigration advisor or immigration lawyer and have them do the application for naturalisation, rather than try to do it on your own.
If you want to be absolutely on the safe side, you should wait until you have had ILR for one year.