I've been doing just that sort of thing for the past couple of days. The BonusInfos.xml has a comment at the top warning one sternly not to fool with mother nature.
The best thing is just to leave it there and not use it for anything. Defang it so it can't hurt, but disconnect it from all function.
For instance, most improvements only have to exist in ImprovementInfos.xml. You can take them out of BuildInfos and UnitInfos, so nothing can build them.
To get rid of biological Bonuses, like Pigs and Corn, I set them all to 0 probability and gave them 90 degrees as both maximum and minimum latitude.
<Type>BONUS_FUR</Type>
<Description>TXT_KEY_BONUS_FUR</Description>
<Civilopedia>TXT_KEY_BONUS_FUR_PEDIA</Civilopedia>
<BonusClassType>BONUSCLASS_GENERAL</BonusClassType>
<ArtDefineTag>ART_DEF_BONUS_FUR</ArtDefineTag>
<TechReveal>NONE</TechReveal>
<TechCityTrade>NONE</TechCityTrade>
<TechObsolete>NONE</TechObsolete>
<YieldChanges>
<iYieldChange>0</iYieldChange>
<iYieldChange>0</iYieldChange>
<iYieldChange>1</iYieldChange>
</YieldChanges>
<iAITradeModifier>0</iAITradeModifier>
<iHealth>0</iHealth>
<iHappiness>1</iHappiness>
<iPlacementOrder>5</iPlacementOrder>
<iConstAppearance>50</iConstAppearance>
<iMinAreaSize>3</iMinAreaSize>
<iMinLatitude>90</iMinLatitude>
<iMaxLatitude>90</iMaxLatitude>
<Rands>
<iRandApp1>0</iRandApp1>
<iRandApp2>0</iRandApp2>
<iRandApp3>0</iRandApp3>
<iRandApp4>0</iRandApp4>...
To keep from upsetting anything, I renamed the minerals in Description but kept the names the computer uses for them.
<BonusInfo>
<Type>BONUS_ALUMINUM</Type>
<Description>BATTERIES</Description>...
Depending on what you are doing you could probably do that and even give them new art and actually use them.
These solutions rancor, making things messy, and I will ultimately fix them properly in the L thing, but they'll do for now.
As for the civilopedia, I haven't done one in civ4 yet, but I would think you can just have the civilopedia entries in the phantom items point to civilopedia entries for stuff you are keeping. It's the same principle as I am using here:
<Type>BONUS_URANIUM</Type>
<Description>URANIUM</Description>
<Civilopedia>TXT_KEY_BONUS_URANIUM_PEDIA</Civilopedia>
and
<Type>BONUS_URANIUMORE</Type>
<Description>URANIUM ORE</Description>
<Civilopedia>TXT_KEY_BONUS_URANIUM_PEDIA</Civilopedia>