I am in a very stressful situation as my application made by post for ILR using Set(LR) has been returned today with 'rejected as invalid' letter. Here's my timeline so far as below:
Application posted: 30th Jan 2016
Visa expired on the same day (30th Jan 2016) : Tier 4 Student visa
HO attempted payment: 2nd Feb 2016 (failed due to insufficient funds)
HO sent a letter asking for new payment method: 23rd Feb 2016
Re-sent the requested information on 7th March 2016
HO attempted on the 9th March and payment failed again due to problems with my debit card

Now today I received my application back with the letter from the HO stating rejected as invalid.
I admit i should have been careful regarding the payment and made using a bankers draft or cheque the next time but messed up as I am currently very depressed and stressed as I am a Phd student and have the pressures of meeting thesis deadline etc at uni and everything has been incredibly hard to manage by myself

I would greatly appreciate if anyone can genuinely advise me what steps should i take next?
- Can i make a fresh application and submit? And is so will new fees apply to me? (in my case £1875 postal)
- I understand that I will be classed as an over-stayer from the date the HO sent me back my app rejecting as invalid......is this correct?
- if i can make a fresh application, is it possible for me to apply via premium service now that my visa has expired?
My application for ILR via 10 years long route has had no gaps of stay or leave in between btw as i have had valid leave throughout the 10 years from 2005, that is, Student visa (4 years):PSW(2 years): Student visa (4 years).