Textures were originally tga format which does not seem great for the web so were converted to png. Seems it should be transparent at some spots but is instead, black. Any ideas what I could try to fix this?
Just to be clear, three.js has a TGALoader which is internally used in loaders like FBXLoader or ColladaLoader. You just have to include it in your project and then you can load assets which refer to TGA textures.
In any event, converting TGA to PNG makes sense since you have much smaller files. TGA files are usually uncompressed whereas PNG files are lossless compressed. So there is no difference in quality.
I only know the converters mentioned in the guide from my previous post. Another workflow which works quite well for me is to upload stuff to Sketchfab and download it as glTF .