I have been in this situation, so please take my answer as my personal experience which I hope is good advice for you.
You have 2 problems
(1) this year you have about £700 less per month than you have got used to and
(2) you have to make serious repayments every month.
I guess you are about £900 a month worse off if say they agree to repayments of £200 a month.
The only solution to pay this back - and one way or another you will have to - is to get another source of income.
My solution was to moonlight in cash in hand jobs, £35 per night delivering take aways (less coz I used my car!) and bar work at times. Then I just outright got a second job, working at a call centre 5pm-11pm.
I survived my one year penalty. I since found an opportunity I wish I had for that year which i will share with you:
http://www.swatuniversity.com/referal/newcareer.php?agentid=189870
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No some hygene points: before you talk to HMCR get your spending history (how much you spend on what) and make a budget (what you propose to spend in the future). When you talk to them you should be the first to make a proposal to pay back say £5k per year over 3 years. Remember to make good points like - I will fininsh paying for my car next year so I will pay more then etc.
DONT admit you have done anything wrong! Just acknowledge that you owe them the money.
Remind them that the reason you were on WFTC was because you are/were a low income earner. You always trusted between HMCR and your employer the correct PAYE would be deducted, and never thought to doubt that or check.
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Dont worry too much. They are nasty but accommodating, the bottom line is if they cause people to declare bankruptcy, committ suicide, go to the watchdog etc they are not doing thier job right. You may be just one person, but as an aggrgate they know they have to accomodate you.
Good luck pal!