The customBG field isn't necessary; the charcode will include numbered items beyond the usual limit (4). So your charcode will contain a parameter such as bg:17. As long as you leave your list of backgrounds intact, the old charcodes will remain "correct". If you're regularly adding and removing backgrounds from the moreclothing configuration list, then your old saved charcodes will become invalid (i.e. they'll load the wrong background when you try to use them).
The hair element works correctly. Your charcode will contain a parameter such as hair:youngtsunade or hair:mouyuu. The charcode treats vanilla hairstyles in the same way as moreclothing-based hairstyles, and it doesn't care whether a hairstyle is static or dynamic.
The swfmod parameter is absent ... but you don't really need it. moreclothing puts everything into categories, such as Legwear or BellyPiercing. If you've loaded a mod via moreclothing then it will appear in your charcode (i.e. bellypiercing:diamond or legwear:tornStockings). Some categories will "stack" (such as body mods - which might include thicker thighs, several tattoos, a replacement set of breasts, etc) but that's okay because moreclothing will just provide a comma-separated list within the new moreclothingbody element of your charcode.
By organizing everything into categories, the mod makes it much easier for a user to manage their mod collection. You can rapidly cycle through fifteen Eyewear options instead of browsing through hundreds of SWF files (and trying to remember which one is the cool pair of sunglasses that you're looking for).
The mod allows you to apply a random set of mods (via the Shuffle button) while drawing on your entire collection -- instead of being limited to the vanilla set.
The mod allows users to extract specific pieces of a mod (e.g. the sleeves and gloves from a full-body costume) so that parts of various mods can be mixed-and-matched together. Similarly: a user can selectively omit parts of a mod in order to create a more revealing version (i.e. topless or bottomless). Without moreclothing, users might need to crudely hack their SWF files in order to achieve the same results.
moreclothing allows individual pieces of clothing to be selectively recolored, even if the original SWF file did not include RGB slider support.
moreclothing allows dialogue authors to quickly swap out a character (or switch to an alternate costume mid-scene) with much less risk of file-not-found errors.
tl;dr - it's a good mod. I would encourage you to keep playing with it. You'll probably find that your initial concerns (e.g. charcode support, confusing config file, longer startup time) will be outweighed by the benefits of the mod.
Edit: since I forgot to mention it. Welcome back!
