Were you looking for a miracle that Home Office would have every possible scenario in which you can apply or not. They will give you one condition and hide other 10. You will get to know how home office deals.
There are so many different conditions of applying for citizenship so I am not sure why you took the test three months in advance when you are not even eligible for citizenship. One of them is to wait for 1 year after you get your Indefinite. You will have to wait that time. If you apply before you will be refused and your application sent back and you will have unnecessary delay. I believe there were some exception to this rule. So if your case is straight forward then you should wait.
At this time Home Office does not have any expiry date for the test so you are fine and have to keep few things in mind. Assuming three months left in your application and you will be eligible to apply around July 1, 2006.
(1) Get ready everything in these three months.
(2) If you are applying on the marriage basis, you will be eligible to apply in 3 years no matter your marriage is still going or not. If not on the marriage basis, you should be applying after 5 years. IN any case make sure you were present in the country 3 or 5 years prior to applying so if this is on marriage basis and you are applying in 1 July 2006 then make sure you were in UK on July 1, 2003. This condition is in Black and white but you will be surprised how many people are refused on this basis. It?s a silly rule that I never understood.
One more thing that you were not out of the country for more then 270 days in last three years and last 12 months you were not out of the country for more then 90 days. This change to 450 days if you are not applying on non-marriage basis. 90 day limit still applies on non marriage basis. Make sure you also complies with this condition. There are some exception to this condition and are clear in the guidance notes for the application.
Hope this gives you some idea.