Oh, sorry to hear that. Hope all is well now!
Ok, that explains a lot. First off your main problem is scab. Captan will take care of it for the most part. However ther is way more to it than I have time to get into. Just do this. Don't put any malithion now, just the captan, than again at petal fall. and at 10 -14 day intervals through June. Scab spores are going to be released over a 6-7 week period starting a week or two ago for most of us. ( what state are you in) You also should apply Before rains as the trigger for the release of spores is rain!
You need to read the label on malithion, I really do not know if 1, it is going to take care of PC, and 2, if it is compatible with captan....! Some things can not be sprayed together, so please read the label.
The flies, I'm not sure what they were. Depending what rootstock you have the trees on, they may just be starting to fruit, and they won't have many the first 2-3 years. Macs and Gala are very susceptible to scab! How well trained are the branches?
Take and post some pics and feel free to pm me, we'll get you going right this year!