[General Questions and Answers] Droidriven:
1) a clean install involves wiping system, data, cache and dalvik cache. All of these partitions must be wiped in order to remove data things that might conflict with the new software that you intend to flash. Yes, you can wipe data and still boot into your ROM. Yes, there are things still on the phone even after wiping the device, but, the things left behind are in partitions that are separate from what you can actually wipe, these other, separate partitions contain all the other stuff that is essential for your device to be able to function. These parts have nothing to do with the ROM that you are using and have nothing to do with what you have installed in your data partition. TWRP does not wipe /data/media partition(internal storage), /data/media is where your personal user data is stored, such as, photos, videos, downloaded files, data from apps such as games, etc. Basically, /data/media contains things that you have stored that are not apps. Your internal storage will still have all the files and folders that were there before you did the wipe. If you want to wipe internal storage, you have to specifically select your internal storage when you use TWRP to wipe the device, it will not wipe internal storage by default. If you still have a custom animation even after wiping the device, it is probably because the boot animation is in your system partition, that can only be removed by selecting the /system partition when using TWRP to wipe the device.

2) Formatting data "should" remove encryption. No, flashing a new ROM after removing encryption will not encrypt the device again unless you specifically choose to encrypt the device in its settings. Flashing no verity only eliminates issues involved with rooting a device and getting root to actually work without corrupting the device.

3)I'm not sure but I think you can encrypt a device without using stock.

4) It depends on which device you have, what your current firmware version is and what you are trying to flash. Some devices require a certain firmware to be installed before flashing certain custom ROMs but it is a case by case scenario. There is no specific answer to this, there is only the question of whether your specific device requires this or a question of whether the custom ROM that you are trying to flash requires this. This is best answered by reading the thread where the ROM is posted, if your device requires installing a certain stock firmware before flashing the custom ROM, it will tell you that somewhere in the thread for that ROM. Whether you need to install the entire firmware or just parts of the firmware also depends on which device you are using in some cases, you might only need the modem or only the bootloader or maybe both, or maybe none, or maybe the complete firmware.

5) As I stated above, there are partitions on the device that do not get wiped when using TWRP to wipe the device. If it wiped EVERYTHING, the device would no longer function at all, it wouldn't be able to power on, it wouldn't be able to boot into any of its modes and you wouldn't be able to flash anything at all on the device, not even it's original stock firmware. There are software elements that MUST remain on the device in order for it to continue to function.

6) It is perfectly safe to use your existing version of TWRP to flash another TWRP version, assuming the new TWRP is also built for your specific model number.

If you have installed a custom ROM and you are having issues, you need to go to the thread where you got the ROM and post your issues/questions there. The users there will know more about your device and what you actually need to do and the developer may also need to fix things in their ROM to solve the issues that you are experiencing.