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XML error: Could not find parent node named "MonsterMash_ADSP_SurgeryFleshAnimal" for node "RecipeDef". Full node: <RecipeDef ParentName="MonsterMash_ADSP_SurgeryFleshAnimal" Abstract="True"><defName>MonsterMash_ADSP_InstallBionicAnimalGill</defName>
but I hope you already dealt with it 
And those 2 mysterious errors revealing with <success>Normal</success> are still there. It's not good but I don't know what else can be done with them now.
About prefixes: it'll matter only in the case that some other mod will use the same names so their contents will depend on the loading order. It may be both for good (there won't be, for example, several different tentacles that could confuse player which one is for which creature) and for bad (overwritten stats could lead to issues). I think the bad consequences in such situations are more probable and would be harder to fix, while dealing with several similar items won't be hard by patching after revealing this issue. So I'd say the prefixes are more good than bad, though are not really required. But at least I'd suggest you to change existing "MonsterMash_" to "MM_"
And if you'll decide to use them you'd better to do it earlier than later so it won't take the extra efforts in the future.Regarding the guide:
1. It'd be good to add an introduction describing what's the point of all this and why working with "dynamically/conditionally created defs" by XML-only means is not trivial.
2. Mention that this method requires using ModCheck (however I think in most cases the checks could be made without ModCheck, by PatchOperationTest based on some unique def existing in Example Target Mod) and ModCheck.isModLoaded is sometimes used for custom messages.
3. Mention the probability of concurrent execution of checks and/or sequences.
4. Mention that using <success>Normal</success> reveals errors that seem to not be harmful, but maybe someone will have some more info on that.
5. Some more investigation could be made for details about what exact differences in operations prevent them from being used in one sequence ("Do not include multiple types of PatchOperation inside of each PatchOperationSequence." but we saw that sometimes different operations worked fine). And probably this info should be put higher, so it'll explain why the several sequences must be created.
6. Other instruments for working with xpath include plugins for popular text editors such as Notepad++ and SublimeText.
Though probably they may eat hay and other things, too, if it's in their allowed area. You can try
So be careful not to comment </Operation> when you want to comment only <li> [...] </li>