Re-Asking Questions not quite answered!

Yes, that is also a good idea. I'm wanting to start off the new rom as clean as possible in order to avoid future disappointments.

When you have multiple patches, they can conflict between the addresses used. As example, two patches which need extra space can use the same address from the unused space in the rom. If you apply the two patches, one piece of the code of one patch will be overwritten by the other.

Editors can also manipulate code or data in a transparent way from the user. As example, if an editor alters the dialogue strings and another patch also manipulates the dialogue strings, a conflict may happen about the modifications.

To avoid this situation, i separate all the rom modifications in small patches and use a tool to detect collisions between them. I use the Dual Patcher for this. Another tools, like Patch Conflict Finder, can also be used.

If you want to begin from zero, i recommend to use the divide-and-conquer strategy. Use the original rom as your base, divide your rom modifications in small patches and use a tool to help to manage them. If your tool can detect collisions or incompatibilities before you apply your patches, it should make things easier for you. You never know when a editor or patch can change bytes where they shouldn't be allowed to do.