I would 100% recommend learning the “manual way” as well so you can understand what tools like MA can do if you mean to do that on a regular basis.
For MA issues, they have a discord linked on their website https://modular-avatar.nadena.dev if you need advanced support.
I would note, ensure that the prefabs that you get with MA are with an armature, if so they will be merged to you armature. If you have a doubt you can always right click on it and redo the “Setup Outfit” action from MA to ensure it merges.
Sometimes items don’t have a humanoid armature, if so you need to use the “Bone Proxy” component to make the object follow a specific bone of your avatar (Hair objects for exemple).
As for modifying parts of your model, you can look at projects like AAO or D4rkOptimizer , they will remove unused objects, so with them if you remove the mesh or mark it as editorOnly, they will “clean” the avatar before upload.
For the texture you have quite advanced tools like TexTransTool to edit texture, but you are most likely having an easier time with an image editor.
I hope you can figure it all out.