Hi there. Sorry to hear about your situation.
The problem you have is that a new master key can only be coded to your ECU using an existing master key. One of your keys that got stolen would have been a master. Don't get confused, there's not a magic master key out there that you can buy for the car and link to your ECU. That means that if you have no keys for the car then your only solution as I understand it is to have all your door locks changed, your ignition barrel changed and a new ECU. This is a dealer job and as you say costs 3000 EURO. It's £2000 in the UK.
The only other possiable solution is maybe to find an IS200 in a scrap/breakers yard and get the ECU, locks and ignition barrel and keys and fit it all to your IS. Still a massive job but should be cheaper.
Good luck.