I want to do a reinstall of Yosemite without losing apps, preferences, photos, and files. How do I do this?

I have a SSD/MacBook Pro late 2011. I had Mavericks on it. I have several backup external hard drives. I installed Yosemite onto one of them to test and see if all my apps worked and my drives for my printer/scanner/copier... all worked. I decided to install Yosemite on my computer SSD... but it was saying it would take upwards of 5-6 hours to download...I didn't have the time...so I got impatient... and copied Yosemite from the external hard drive to my SSD/MacBook Pro using Carbon Copy Cloner's latest version. The SSD/MacBook Pro was bootable and all my apps worked along with my driver. Only problem is that the SSD/MacBook Pro takes so much much much longer to boot than before. Is that Yosemite's problem? or is that because of the way I installed Yosemite on my SSD MacBook Pro? Will installing Yosemite again the proper way fix the boot up time problem?

Re-installing Yosemite via the App store saved all my apps (they still work)... saved all my files and documents...etc... on my computer and now the boot up is very very very quick compared to before...also quicker than with Mavericks...and much quicker than my external hard drive with Yosemite!!!! Wasn't that complicated after all!!!!

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