So I got everything going good and got the game to run but the combat runs very sluggishly and slow compared to before.
Yes, if you continue reading the guide from where you left off, you will find the solution to that issue as well. FFNx prefers to use DDS texture format, and most of the catalog mods have not yet been hosted in that format. There are things you can do to help with the issue if you would rather not go through the effort to convert you modpack to DDS.
First and foremost, DISABLE the "60 FPS Battles" mod located in the "Animations" catalog IRO. This mod is severely incompatible with FFNx and it is also very poorly described as to what the mod actually does. It is not worth using in any case with FFNx so that is the absolute first thing you should do. I need to amend this information into the guide, and for that I apologize.
If your game continues to not perform as you would like, turning down the resolution and or the internal resolution scale options in ffnx.cfg can help with performance, as well as switching the backend renderer to Direct3D11 instead of OpenGL (with some cards anyway, especially AMD card will benefit from this)
If the problem persists after all of that, then you have no choice but to switch your mods to DDS format. All of the information needed to do that is in the guide, so make sure you please read the guide in its entirety. Like I have said from the beginning, if you follow the guide front to back correctly, you will be very close to the most optimal performance you can get out of (non-reunion) modded ff7 right now.