If you are keeping it forever then that's not so bad, but worth keeping the original engine and any parts you remove as should you wish to sell it in the future you have the correct parts to offer to any potential new owners. As these cars get older it'll be the standard ones that fetch the ££££, look at RS prices the standard ones fetch a lot more than the messed with ones.
As you say great that the interior is in good condition as interior parts (especially seats & door cards) are very hard to find in decent condition now.