Water penetration

We have lived in our 3 storey, flat roof townhome for 2.5 years (built in 2015) now and we have had water penetration during heavy rainstorms or snow melts 5 times now spread out over the 2.5 years. The leaks have been in 3 different locations - 2nd floor bathroom ceiling, main floor kitchen ceiling and wall outlet in kitchen. The top floor has had no leaks. The leaks never occur at the same time - but they are all along the back wall, which also has a sub roof along the 2nd storey. The back wall is stucco - there is no visible cracking or bulging. We have had a roofing company come and replace a whole section of membrane on the 2nd storey sub roof , re-do vent flashing on the top roof. We have also had a handyman come and caulk all external venting and windows. We had downspouts cleaned just a month ago. Thousands of dollars and leaks are still occurring and we don't know where it's coming in. We got a quote from a leak inspection company for $2,500-$5,000. That price seemed...high. We are hoping we can figure this out without having to pay that kind of money just for the inspection. Or is this just the kind of cost we are realistically looking at to finally resolve the issue?