I'm not sure what went wrong with the Kies update, but as far as I know, there is no easy way to correct the problem. Actually, most of the people who frequent this forum are using custom firmware, rather than stock. In general, when things go wrong with a flash, (or update in your case), it is much easier to just re-flash. Of course, if you are an experienced developer, you can look at the log files and determine what went wrong, but even then fixing it is questionable.
You will most likely find that if you perform a wipe data/factory reset in 3e recovery and then perform a fresh Odin install of the firmware, you will have no problems. You can stay with the stock 4.1.2 UCMD8 firmware, or you can install the custom firmware of your choice. If you opt for custom firmware, there are a number of choices. Since you are accustomed to running stock, you may be more comfortable with a rom that uses Samsung Touchwiz as a base rather than one that is based on the Android Open Source Project (AOSP). I run SHOstock3 which is modified from the latest Samsung firmware for the International SGSII and is also 4.1.2 based. It is extremely stable and has many many features that you do not have with stock.
Since you are rooted, you should install Titanium Backup and do a complete backup of all your applications in it. You will then be able to restore application data so that you don't lose anything. With it you can also restore your SMS & MMS messages, and possibly wifi access points, call logs, and bookmarks of the stock browser. I'm not sure about the last three if you would be changing to a different base. I think the call log would restore from stock to SHOstock3 since they are similar applications.
If you will be flashing firmware in the future, you should consider purchasing Titanium Backup Pro, which gives you batch restore along with some other features. It is very tedious restoring things one application at a time.
Also, before you wipe and re-flash firmware, you could first install a custom kernel and do a nandroid backup. Titanium Backup will read and can restore things selectively from a nandroid backup so you would have access later to additional items if you need them.
Hope that's helpful and if you have any questions, just ask. You can find a lot of resources in my signature, including a link to the Download Repository.
Oh, and the call log is not your address book. Titanium Backup will not restore that, but you can save it in Google and restore it from Google which is what most people do, or I believe you can find a stand alone backup program for it.