Long Residence (10 years) for Wife, I am BC

[walana]

Hello experts...

I wonder if someone could help me?
My wife completed 10 years (mostly as my spouse) in September last year. She now passed B1 for English and also life in UK test and we are looking to apply soon as her current leave is running out end of April 2017.

Due to some issues with her immigration history i am in two minds, should i apply for extension or go for ILR..

Here is a brief history;
She joined me in UK on 26th of September 2006 as a student spouse.
All good until August 2011.
Together we applied for extension of student visa student/spouse.
UKBA granted me extension but rejected her application saying, they weren't able to collect fee from her account!!!? (She clearly had enough funds in her account)
We still had time so this time decided to send them postal order. Before sending her application, i personally phoned HO to inquire, should we send discounted fee because the original application was joint or full fee, i was advised (over the phone) that because it was joint application to start with, we are eligible for reduced fee. (Due to nature of conversation i obviously can't prove that now).
Once again application was rejected!!! saying that correct fee wasn't sent with the application! how awful!!
This was end of 2011 (23 Dec 2011, xmas eve), we weren't able to resend the application because her leave was expired for more than 28 days, we weren't able launch the appeal in time due the holiday season. we appealed 1st tribunal but it was rejected that it was out of time, 2nd tribunal took the appeal but decision wasn't in our favor.
Cut the long story short, they started sending One Stop Warning. We started to receive letters from Capita on behalf of HO, asking my wife to leave the country. We kept responding to them via our solicitor. The finally gave up and granted my wife 2.5 years visa on family/human rights ground on 3rd April 2014.

I am now British citizen and so is our 6 years young daughter.

I know its so much information but my question is simple, in your opinion, do my wife stand a chance to get ILR or we should kept going we 2 more extensions??

Many thanks
Walana
** oh, her current nationality is Pakistani.

[vinny]

If they maintain that she had overstayed for over 28 days, then it's likely that they will refuse a Long residence application.