Hate to tell you this but the 2009 model MBPs were built, assembled, with a very cheaply made HDD to Logic board cable and your original drive may be fine and the cable is the thing that is failing.
I suspect this because once a drive fails it is near impossible to get any useful data off it. So if Apple was able to copy your files from the old drive to the new one that drive is probably still OK. And that you are now still having problems with the brand new drive.
No the problems you are having can not be caused by just having corrupted files store on the drive. The only files that are accessed by the operating system, while booting and running the computer, are those operating system files and whatever programs you are running. even if a program access those corrupted files it would not cause problems with the OS but may crash the program that is opening them.
As for TM not working that again is a sign that the cable is bad because TM can't copy the files to its backup over that bad cable.
Wow. Your explanation certainly seems to be accurate. Because, the sort of problems I am having now are very very similar to the ones that I had with my previous HDD. (1) For example, while copying large files from an external HDD to the MBP HDD, it randomly begins to freeze. (2) Even after fresh reinstall, time to boot continues to be very high (3) Unpredictable freezing while working in Mail.
I guess, I will just take it back to Apple Support (or perhaps call them tomorrow). I appreciate the time you have taken to explain this. One last thing if you have the time: do you think I can just tell them (at Apple service) that the cable might be at fault? Thanks again!
Yes of course. When you take it back in explain to them that you are having very similar problems with the new drive as you had with the original and that you suspect, and have been advised, that it is more then likely the cable from the HDD to logic board that is bad and or failing. Ask them to change the cable to see if that corrects the problem and or Test the cable for failures.
There are many posts on this forum about the 2009 MBPs bad cables. Most of the time people have done what you did and replaced their hard drives to be greeted with the same problems. Once they changed the cable all the problems went away, even when using their original drives that they thought were bad.
Good Luck & Best Wishes.
Your assessment of the problem was spot-on. Much appreciate your input in this! Today I went to Apple Service and they changed the cable as I waited (for free even! of course having charged me a bomb for that HDD and the labour cost for the same previously, I was not particularly thrilled, but anyway). I came back and starte it: boot time is half as before, time machine is already runnign half way, applications open faster, no spinning wheel of death yet! It was indeed the cable!
Glad to hear it worked out and you now have it back up and running.
As there is no test for just the cable any problems with that will show as Hard Drive problems. I believe, but not sure, Apple knows full well of the faulty cables used in that year MBP. But as with Apple they keep that stuff private as to do otherwise would mean that Apple would have to admit they use cheap parts in their computers they charge an arm and a leg for.
Good Luck & Best Wishes.