The reason it doesn't work is you have partial sprites for them. Ultimate Doom doesn't have those sprites but ZDoom doesn't care about that (it basically treats Doom 1 & 2 as the same game) so it spits out an error because it goes, "Hey, there's some Chaingunner sprites here but not all of them, and there totally should be."
The easy fix is to, of course, just include all the Chaingunner anims that you don't have in the mod. This is a messy solution and breaks a few generally accepted "rules" about how you're "supposed" to do things in a mod (although Xaser's 5th Episode had the Mancubus and Revenants in Doom 1 verbatim). Mind you, if/when you get around to doing a Smooth Animated Chaingunner, the problem will disappear.
Most of the Sprite Fixing Project is stuff like fixing offsets for monsters (a lot of them seem to have been automatically generated; makes a lot of sense but doesn't exactly make them look as good as they could be) but also there's some minor stuff like, for example, Baron and HellKnight hooves change colour from frame to frame sometimes. I'm not sure if the error is present in your versions.
I dealt with some of the key problems you're mentioning when I made a small personal mod to replace the skull keys with some rune keys from Quake. (I'm doing a side project with Quake bullshit.) I wanted to keep map compatibility, just replace the skull keys with the other keys, but I wanted to redefine them instead of just replacing the sprites.
The solution you're looking for is in a lump that you wouldn't otherwise normally touch called LOCKDEFS. Check the Wiki:
http://zdoom.org/wiki/LOCKDEFS
My solution was simply to use ClearLocks at the start of my LOCKDEFS file and then basically redo the original Doom lock defs with slight differences.
So for example, here's the default RedCard lockdef:
Code: Select all
Lock 1 Doom
{
RedCard
Message "$PD_REDC"
RemoteMessage "$PD_REDCO"
Mapcolor 255 0 0
}
All you need to do is, after using ClearLocks, define this new lock:
Code: Select all
Lock 1 Doom
{
NewRedCard
Message "$PD_REDC"
RemoteMessage "$PD_REDCO"
Mapcolor 255 0 0
}
The Doom locks are already tied to the numbers ("Lock 1" etc.) so by re-defining them with your new actors (NewRedCard) it'll work perfectly with almost all existing maps. (The only ones it'll conflict with are, for example, ZDoom levels with their own LockDefs lumps. But that's a given, isn't it?)