1. I don't have a definite answer to your question, but I think it is almost inevitable that there will always have been a time limit of some sort on making contributions.
2. However, if I have understood you correctly, you are saying all the necessary contributions were paid but some were paid over 6 years late so are not being taken into account for the pension. It seems to me that in this situation it is quite wrong for the Contributions agency to keep those contributions - they should repay the money to you (& you could then use it to help pay for the Class 3 contributions you need to make). I suggest you make a formal complaint to them about this, & if they say they are entitled to keep the money ask them to quote the specific Statutory Instrument or other legislation which gives them that right. If not satisfied, you can complain to the Independent Adjudicator. See the HMRC complaints leaflet here:
http://www.adjudicato....uk/pdf/factsheet.pdf
3. Apart from all this,what you say looks rather like fraud or very serious error on the part of the accountant. Have you considered a claim against the firm he/she was working for? Or if the accountant was a sole trader are you still in contact because he/she should have had insurance against this sort of thing?