Apples and picture scrambles

I was going to post a couple before and after pictures of projects that I have worked on lately regarding spray paint for one and a sisal rope for another.  But the mad picture scramble on this computer is making it impossible.  
You see at the beginning of the summer our computer almost crashed, well it did but my brother-in-law fixed it and chased away the nasty viruses.  When I got it back my pictures were no where to be found.  He said it shouldn't be a big deal since he didn't delete anything and even if he did that is usually recoverable as well.  Great! I thought and he recovered all the pictures!  Even better I thought.  Until I got the computer back only to realize that my meticulously organized folders were gone and there 8,000 give or take pictures in one large folder, and in no particular order.  Well it seems each folder at least stayed grouped together, but I think he recovered ALL of the pictures that have ever been on this computer- so all the blurry ones I had once deleted have reappeared.  On top of all of that, ALL of the pictures are at least duplicated if not copied up to eight times on some of them.  Phew! at least I didn't take 8,000 pictures!  The weirdest thing is the computer still acts as if these pictures and folders still exist.  Like if I go to add pictures into my folder labeled 'crafts' it will tell me that folder already exists and then it will ask if I want to merge the folders, of course I want to merge the folders we don't need any more duplicates.  It whisked my pictures away to said 'craft' folder.  And now I can't find them.  I mean if I do a search for 'craft' folder I can find it but I can't seem to get them to where I can use them. I have even tried to follow the trail when I go into the place where it asks you where you want to save them.  It seems simple but as soon as I try to find them, they don't exist.  So if you are still reading this complicated boring computer problem and know how to help, would you like to set up a 'help Jenn fix her pictures' date?  On the bright side I only have 1,890 pictures left to sort through.  Even our back-up hard drive is messed up with a couple of 'layers' of saved info.  I want to just get these organized saved on a hard drive, and then start fresh with our brand spankin' new Apple computer.  Now I have all sorts of new things to adjust to.  Now back to that picture disaster, and if you are an expert on saving and organizing and computer glitch fixing, I am serious about needing help.