As far as I am aware it is only an 8bit version number (2^8=256 combinations: 0-255) and the effort required to increase said number would likely be astronomical* (such a value is likely contained within a header and given IOS are a fairly low level part of the system it would likely involve changing the IOS loaders for absolutely no gain (assuming you are sensible and do not update).
*you might be able to make a kind of secondary loader/parser (think a tweak geckoOS) able to read an IOS module altered in such a manner but frankly why bother.
I know you said it was not your intention but while I am answering questions I might as well: installing as "unused version number", it would not be all that difficult for Nintendo to do things against unusual version numbers (quite in fact a cIOS was overwritten in the 4.0 update (patchmii), just not the "useful" ones).
cIOScorp on "unhackable" wii, afraid I have not read up on the reasons behind the "unhackable" wii yet but if indeed any bricks are simply caused by old IOS modules causing problems (earlier versions lack features or something) with new hardware/software/checks in the "unhackable" models then I can see no reason why using the new IOS as a base for further hacks would not work.
Original topic: to my knowledge no "all in one" tool exists mainly as it is fairly pointless. If you did want an all in one tool then I suggest looking at the cIOS installers (online versions) and/or patchmii core
http://wiibrew.org/wiki/PatchMii , One designed solely for IOS36:
http://wiibrew.org/wiki/CIOS_Patchmii_Installer you appear to want a more generalised one though.
I can see no reason why anyone would do this though when stuff like the various cIOS modules exist.
If you wanted to go in manually I am pretty sure the tools exist:
step one would be get an IOS module in wad form (NUS downloader if you do not have one:
http://wiibrew.org/wiki/NUS_Downloader )
From here you can unpack or otherwise change things (most tools like the IOS36 one above do it on the wii) and repack to wad.
Install as you normally would.