My 46 was literally scrap so I had no qualms about doing my own thing. However, I knew that by going that way I was going to spend more money, and end up with a car worth less, than a stock build. Just something to keep in mind. If you are interested in having your cake and eating it as well, either a stock restoration or a 47 conversion would be the way to go. Either would give you a fun car to drive and reasonable resale value. No, you won’t recover your costs unless you count all your labour as donated.
If you go the 47 route, please do not fit a Mazda rotary. They generate enormous amounts of heat, a problem in a Europa, and, frankly, nothing says slap-dash more than a Mazda rotary conversion. I’m sure there are many good ones out there but they have a reputation in the business.
Finally, you have corrosion in your chassis, very normal in a 46. You are going to have to remove the chassis in order to deal with it properly. There are three ways to go: cut it out the bottom, cut out the firewall and console and take it out the back, or separate the two chassis halves (bottom and top) which was how they put it together at the factory. It will be a lot of work and you would have to do it again if you subsequently decide to convert it to a 47. I would decide on that and only change the chassis once.
Anyway, nice car, good project, and all the best. I absolutely adore my 46.