What are my chances of applying to naturalizations?

[ukeagle]

Hello everyone,
I came to the UK in 2000 with a visit visa and applied for asylum in the airport, was given a temporary admission and told to wait for a decision.
They refused my asylum claim in 2006, I appealed and was granted 3 years discretionary leave outside immigration rules.
In 2009 I was supposed to renew my discretionary leave but due to serious family issues I completely forgot to renew my visa and remembered 2 months and 10 days late!
Immediately I applied by post and just wrote in the notes of the form that I am sorry for applying late and I was very ill.
I did not hear from the home office back for 2 years and 11 months! I involved the MP and the home office replied saying they have so many cases and I should hear from them soon and they also mentioned when they have received my application (they did not say late or anything they just note the date they received the application)
A month later early 2012 I got my extension for another 3 years which expires on 2015
On 2015 I applied on time and I had 2 options in the form to choose from either ILR or extension to my discretionary leave. I choose ILR. After a few months, I was granted another 3 years of discretionary leave instead of ILR.
Last week 09/2018 I applied for ILR using premium service and was successfully granted.

I am worried about the delay in applying in 2009, can this cause naturalization refusal?

Can someone kindly guide me, please?

Many thanks in advance

[ukeagle]

anyone, please?
my question simply: from which date does the home office count the 10 years good character, from the date they received my 2 months and 10 days late extension application in 2009 or from the date they grant me in 2012?

[CR001]

You were an overstayer till your DLR was approved in 2012, thereby unlikely you will be successful with citizenship until 2022, 10 years after the date your stay was granted.

It was not an HO mistake that you submitted late, it was your own and your late application was submitted more than 28 days after your last visa expired.

[ukeagle]

Thanks, CR001 for your reply,
I have a genuine reason (family bereavement) for the delay in applying would that be considered if I show some proofs?