When you recieve your phone stock it is odexed, meaning that the system apps are split in two, an .apk file and .odex file. both are the same application just split in two.You can view this by going to the /system/app directory with a root file manager, you will see your apps(apk) with their odex counterparts;for example sms.apk and sms.odex. they do this so that booting is faster and it saves more space then having odexed files. When your phone boots it uses the odex files to anticipate the applications that it will be using so once the phone is on they are immediatly available, making your phone faster upon starting.
Deodexing is the process of taking the odex file and recombining it with its apk counterpart. This only slows the phone down upon initial booting since the phone does not know what apps are there it will act sluggish at first. as you use the apps it will create whats called a dalvik cache and the phone will become more responsive and quick as it is suppose to be and upon next booting it will have built up this dalvik cache so it will know what to do and what to anticipate.
Why is deodexing necessary? in order to modify an app it needs to be in one piece otherwise changes to an apk would be difficult since you would need to modify both apk and odex file piece by piece. By deodexing you can make modifications without difficulty (relative to your skill set). All custom roms are deodexed so that themeing to phone can be done, such as color layout, fonts , sizes can easily be made.
If you flash the stock rooted rom that i directed you to earlier, you should not lose any of your current data or settings since that rom same as your stock rom but the .apk and .odex files have been recombined.'
I hope this answer is clear enough