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I got a tremolo solution like in the image, this is the mounting base. The tremolo was sitting to low so i glued on two pieces of oak on either side early on in the building process. Now I find that i need them 3-4mm higher so I dont need to adjust the bridge saddles so high.

I cant decide if i should just remove the oak pieces and put in new ones (its glued with hide glue so should be easy to remove). Or should I glue on some rosewood veneer? Does it matter in any way? The cavity is hidden away by the the trem unit.

Shouldn't matter a bit. Remember that getting the geometry right is the first and most fundamental part of building a guitar. Make sure you have adequate range on all of your adjustments to set all of the action parameters and have some wiggle room for the future. It looks like you have some solid modeling software there which will help but I like to mock things up with the actual parts to make sure.