I am pleased to confirm that my wife has been granted ILR, it took 3 months but the anomaly with her passport middle name and that on our marriage certificate being different appears to have not caused a problem and late submission of the passport was also accepted as her application was submitted prior to the expiry of her FLR.
One question we have is that the ILR has an expiry date of 2024, can we assume this has to be renewed then unless we go down the UK citizen route which would then override any expiry date ?