ILR Doubts

[aloks_01]

I am in UK since Sept 2003, came on student visa and then shifted to HSMP in Oct 2007 and got first extension in Oct 2009. Now i am due for my ILR in Oct 2012.
I have got married in May 2009 but partners visa was rejected due to marriage date issues but cleared after going through tribunal in March 2010 and she joined me at the same time.

My partner returned to India in July 2011 due to her job. I left my job in Feb 2012 and became self employed and took one assignment of UK based company to work in India on contract basis.

Since Jan 2012 I am in India and working as a contractor for UK based company and getting paid in my UK bank account by raising invoice to the company. I am making sort visits (2-3 days) to UK in every 80-85 days as i dont want to break the 90 days rule.

I have few questions from forum members and any help will be really appriciated:

1) Total number of days out of UK is crossing 340 days in last five years in which 248 days are for self employment work in India, will that affect my case ? if yes then how can i avoid this or what letter is required from the company for which i am working as a contractor although i am not breaking 90 days rule.

2) My wife is out of UK since July 2011 and she was on dependent visa, will this effect my application ? although i am just applying ILR for myself.

3) what paper work is required as i am showing employed till Jan 2012 and self employed after that.

Any help or suggestion will be really appriciated......