I think the method you suggested is the only fair way to do it, however, instead of allocating 35.5% of the $45,000 against the rental portion of the property, I think it should be 35.5% of the total renovation cost of 50K that should be allocated to the rental portion.
Another idea would be to use data on what percentage of home improvements are recouped when they are sold. For example, if your 45K was for a kitchen, and say people recoup 70% of that (just a guess), then take that percentage off the home sale cost. I will add an example.
