I can't be sure on the terms of this deal, so all of this advice is based on a lease deal I had a few years back. So if I have this wrong, apologies in advance. But if this is a standard lease deal like I had, you will indeed be 'losing' your £3000 as it's the down payment on the car.
You are also signing up in blood to £330 x 35 = £11,550.
So, after 3 years you will have given them £14,550. You will have had 3 years motoring. At that point, you can either give them the car back and walk away with nothing (your deposit is indeed lost) or you can give them £13,000 as the balloon payment on the car. If you are doing this, your final outlay for the car will have been £27,500. It's a good price for a car of this nature if you've financed it.
So at this point you've got a 3 year old car with X miles on the clock. You can run it for as long as you like or trade it in. Look at what you could trade it in for vs a new one. Will you get back the £13k out of the dealer? Maybe. Maybe not. If you get £16k back from them, you've had 3 years motoring in the car and in depreciation it will have cost you the monthly payments (£11,550).
Another thing that concerns me here is this..... if you are saying you cannot afford to push the payments any further upwards, how are you going to afford to save up the £13k balloon payment over the 3 years? That's another £360 per month you'll have to put aside so as you can actually do anything with the car other than give it back at the 3 year point (and in giving it back you've lost your initial £3k and you've paid them the £11,550 over 3 years) Unless you know you've got a lump sum coming, this could be an unhappy experience!
Take a look at the APR on this deal and go along to the moneysavingexpert website. If you have a decent credit rating (which you'll need to get the lease anyway) then look at bank loans for this. What I'm getting at here is if you CAN aford to pay the extra that you'd need to save anyway then you'll get a cheaper deal on a bank loan to pay the full amount over the 3 years. Even if the lease deal is good, you really really really need to make sure you can cover that £13k at the end!
Also, look into finance gap insurance on this - if your car is wrecked then your regular car insurance may not pay out enough to cover the amount of finance you owe on the car!
For me, the lease worked out well - I was getting a car allowance from work instead of a company car and it covered the monthly payments. I had put down a couple of grand up front and I then had a balloon payment of £7k. My B6 A4 has been run for another 3 1/2 years after this and is now my wife's car. We've had our moneys worth.
Moving onto the spec..... As to features etc, look at the Audi config tool on the website. It may have B+O (Audi don't do Bose anymore). But look at the regular SE spec price vs the SE Exec and decide if the extra is worth it or if you could go for a different engine etc rather than the exec spec. Spec yourself a car worth £28,500 and then (once you've got yourself sorted with all the finance stuff above) go and see him and tell him you want that YOUR spec of car for £25,500 with the rest of the deal he has offered. Be willing to walk away. If he sees you dribbling then you won't get it
Hope this helps
Gary