Welcome to the boat mate.
TMO and RFB are the biggest super mods and there are versions of RSRD and OTC to use with each. You can't use TMO and RFB together, one or the other. They have environmental mods incorperated into them so don't use any environmental mod with them.
Pick your supermod and add any patches and load that first.
Than load the proper version of RSRD if you want to use that.
Next load OTC if you use that. If you don't use OTC you can use Max Optics and SCAF if you want.
You must read all the documentation for each mod.
Put in each mod one at a time and run the game to see how it works and than add another if all is ok. Keep it simple till you see what is going on.
From this point on there are so many mods it's impossible to make any list.
Best advice I can give you is to make a clean install and before you do anything else make a copy of the Data folder and keep it safe, if things get messed up and they no doubt will, all you need to do is copy the safe data folder in place of the old one. All mods work in this folder. JSGME does a good job keeping track of things but even it has limits.
Install the game in a new folder not program files folder.
Do not use the default SH4.gu to launch the game but find SH4.exe and use that.
I myself use TMO sometimes with RSRD sometimes not.
Right now I'm using SCAF and Max Optics, bad eyes.
When I finish this career going to OTC.
Others I use are
EAXsound
Map labels 1.3
Webster's better air patrols
OPCFv1.2_yellow_SCAFfor1.5
That's about it.
Good luck and good hunting
Magic