Some thoughts to keep in mind as you begin running games in L5R, in no particular order:
Unlike most RPGs, the player's characters are samurai who exist to enforce the status quo of the world, not to buck it. The samurai stand to gain the most from the world of Rokugan and its social structure, and any samurai who would openly rabble-rouse or perform acts for their own monetary or personal gain would become outcasts. This is the biggest hurdle for new players to get over, compared to the roles of their characters in other RPGs.
Make sure that the PCs have a reason to be together. Whether that means they are Emerald Magistrates, their assistants, or all from the same clan, having a reason to pal around with these other samurai is important in making the stories credible. Why else would a Scorpion, Crane, and Lion all want to hang out and get into trouble together?
Avoid random combat encounters. Combat in the game is swingy, and if you put your PCs through enough combat encounters, sooner or later they will draw the short straw and it will end up bad for them. If a PC is going to die, they probably won't want it to be at the hands of Random Bandit #418.
If you plan on having your players fight someone, they should have a name already. This is my rule for myself when planning encounters, and ensures that the combat serves the drama of the story. Any samurai they fight has a personality, mannerisms, and dozens of ancestors behind their swords as well. Basically, killing mooks isn't as dramatic as killing Isawa Motoro, the daimyo's trusted advisor. Drama is what L5R does well, do your best to make that happen.
Try to make your preparation structured. I find myself to lean a lot into improvising things as a GM, but I don't think the "free-form make it up as you go" approach leads to very satisfying stories in Rokugan. I would err on the side of over-preparing until you understand the way the system works. Having finely crafted plots serves the goal of achieving high drama better than winging it on the fly. The "three-act structure" is your best friend here.
Try to include a moral dilemma in each adventure. Rokugan's society was designed to promote this. A cheat for this is to look at any of the two tenets of Bushido, and put them at odds to make the players pick one of them. Is it better to be lie and keep to your Duty, or forsake your duty to be Honest? Should you follow your lord's command when it indirectly means the death of dozens of innocents? A treacherous enemy has requested the right of seppuku, but you need information from him. Do you deny him his right as a samurai to further your own goals?