[AT&T Samsung Galaxy S 4 Q&A, Help & Troubleshootin] Mamputo:
Hey there! Here is my take on at least some of your questions. I am not a super pro, but I will try not to give you any wrong info.

1. The zip files that are still out on your SD card are just the install files for whatever you are flashing. They won't be cleaned up automatically and you will need to delete them yourself if you want them gone. That being said I would recommend leaving the previous version's zip out there in case you need to back out of the new version.

2. If by phone settings you mean all of the settings in the various option menus baked into the ROM it is best to redo those when switching between ROMs. Many ROMs add and take away options and add whole new option sections so you will want to go through those and set things to your liking. Another option is to use a launcher like Nova Launcher that lets you back up its settings and restore them which is a big chunk of the things I change when going to a new ROM. Some people may have a different opinion on this one.

3. Yes if you make a backup in a recovery like TWRP and then restore from it it will be like you never flashed the other ROM. Titanium backup does what you say and also can backup individual Apps themselves and restore them.

4. Once you have a recovery installed you should not have to go through the hoops you went through to get it there to update it. Check the thread for the recovery for upgrade instructions.

5. Your SD card will not be wiped when you wipe system or data. There is also the internal "sdcard" that if I recall is not wiped when you do a standard wipe which will keep things like pics and videos between flashes.

6. So you were trying to access the phone storage/SD card while it was in recovery? I have never had much luck with that. I always just make sure I have all of the files I will need to install the new ROM moved over before I wipe it. That being said if you have the right driver it might be possible.

7. Titanium Backup, a file explorer that can leverage Root access like Root Explorer, maybe something like Greenify (I think it takes Root). Other than that check out the thread in the Apps/Themes subforum where people list their top 5 apps.

8. Pass (but I think what you heard/read is right)

9. Goo Manager can let you know if there is updated version of your ROM or what other ROMs are available for your device and download them. It can also be used to install a recovery. Personally I don't use it and just check ROM threads for updates if the ROM doesn't offer OTA updates.

10. I rarely see mention of security fixes/features in custom ROMs so I don't think you need to stay on top of threads for that reason. With that said, if security is crazy super important to you then a custom ROM might not be your best bet. Even though source code is available for most if not all of them that doesn't mean someone has gone through the code looking for security flaws (or even malicious code).

11. You can test this yourself. Go into the "Apps" section of the options and look at what Apps are running then swipe one away and check again. Personally I would go ahead and swipe away Apps as needed since that is a core Android feature. I haven't seen a mod for what you are asking.

12. The other two TW-based ROMs I have used are Goldeneye and Alpha. Both are good, but I am using Alpha now due to its higher degree of customization. Goldeneye hasn't been updated in a month or so, Alpha is being updated regularly at the moment.

---------- Post added at 08:15 PM ---------- Previous post was at 08:09 PM ----------

Here is the link to the thread where people list out their top 5 apps!