today I was looking at my rubicon, and I noticed a bolt is missing. On further inspection I noticed there are actually 2 bolts missing, but I don’t know what the part is or what the bolts do, so I’m not sure where to start on getting new ones lol. Any help would be GREATLY appreciated!

 

I can look on my tonight if nobody responds. i do know there are some threaded ports on that 3.6L that are not used. it seems there is one on the driver's side in that same general area. i don't see the 2nd one you're referring to.

 

The second hole is forward behind the oil dipstick mount. I have searched some photos on the web and found pics of 3.6 pentastar engines with the same two holes unused. Maybe they're for a different emission system setup. These engines were used in many,many different applications.

 

yup. keep in mind lot minivans with this engine it's sitting sideways for FWD. These are likely mounting spots for something in that application.

 

Common thing for engines or even cylinder heads that are used for several different vehicles.
Looks fine to me.