Okay so... I finally corrected any positioning mistakes I made earlier in my building mod, fixed the navmesh to the best of my ability, added all the finishing touches /etc/. With one thing left, to turn the Esp to an Esm. I did so using Fallout Mod Manager, OpenTesnsip or something like that. It was very very easy making it into an esm. The Esm is running mostly okay, but there is one problem. The objects in the vanilla cells one inside the Novac motel, and one inside of a misc wilderness cell, well they are kind of glitchy. The glitch type depends on these situations. Basic explanatory context: It adds a trapdoor to a secret basemant under Novac's bathroom, which is concealed behind a tub, which in addition is concealed by a curtain, and lastly concealed by a movable stack of boxes. These two glitches only effect objects added by mods inside of two vanilla cells, and all the other cells the mod adds, or the other vanilla cells aren't effected.

Esp only: The location of all the objects/items is just fine no of the glitches listen down below. Only thing is ideally, I'd rather use an Esm than an Esp.

Esm only: Completely game ruining glitch the tubs multiply, and unevenly clash together. The curtains are not there, activating the trapdoor is nearly impossible though can be done.

Esm+Esp: A few rather annoying glitches though not nearly as bad as the Esm situation. Getting through is easy. The glitches are very mild/nothing game breaking though still less than ideal. The boxes to a limited extent multiply inside of each other, which makes removing them more annoying, and they crowd the room more, separating them takes a little time, and of course ow the immersion. Also present in this situation: Some of the sniper rifles on the two balconies I made are a bit misplaced. This is annoying though by no means game ruining unlike the Esm only situation, as they are still easily accessed/the positions still make sense, but ideally they would be located exactly where they were when it was an Esp before hand.

So what's it sound like the problem is? I am extremely new to converting Esps to Esms, and I also have my Esp file before the Esp to Esm conversion safely stored elsewhere just in case I did something really bad. Did I not use the right thing to convert the Esp to an Esm?

You should use FNVEdit to toggle the esm bit, so that the ONAM records get updated. ONAM records are the vanilla records that your mod is over-riding. I don't think tesnip does it.
Also, if you are going to change the extension of your plugin to esm, do a clean save with your mod unselected before testing.