You are under what is termed 'old rules'.
Means you are eligible for ILR after 24 months living in UK.
You arrived in UK July 9th 2012
Means your 24 months qualifying period will be completed July 9th 2014
But you are allowed to apply UP TO 28 days before the anniversary date of July 9th 2014
Means the very earliest you can apply is July 9th minus 28 days = June 11th 2014

You spouse visa expires on 29th September 2014
Means you can apply for your ILR anytime from June 11th 2014 until 29th September 2014 (of course you shouldn't wait so late as 29th sept)

Concerning your holiday, don't be worried. there is no restriction on absences from UK as far as ILR is concerned.
It will only count when you apply for British Citizenship. Even then you are allowed 90 days per years out of UK
So no worries at all.

Hope that helps