Engine replacement

Hi I have a year 2000 Audi 80 cabriolet that has a massive flat spot I bought it a few years ago from a chap that owned a garage and he was unable to sort it I used it for a year and during that time change countless parts including plugs leads air massive valve air filter all the obvious things but nothing since then it's just sat in my yard. It's such a lovely old motor that I would really like to use it this summer and I was thinking about sticking a 2 litre engine in it as the 1.8 is a bit gutless. I have the facilities to do this and was wondering if anyone has done this or has anyone got the miracle cure for the existing engine. Cheers Stuart