How to add grounded junction boxes when installing recessed lighting?
For jobs like that I am very fond of EMT conduit.  It's a semi-improved space so it's a good fit.  You lay the conduit (the metal conduit is a legit ground path) and then when it's done, you run the wires.  The material cost is pretty good except you'll need a $30 bender and waste a stick or two of 1/2" conduit tube until you get the hang of the tiny offset bends.  

However, EMT inherently connects the grounds of all those locations together, and 

Don't "island" grounds

I heard you mention that your house wiring has no grounds, and your receptacles are grounded "to the box".  That only works if the box is grounded!!  and "grounded" means all the way back to the main panel to the neutral-ground bond and the grounding electrode system (the intertie to ground rods or water pipe). Otherwise, it can work against you.

Consider this.  Imagine a 2-socket outlet that is grounded "to the box", but the box is not grounded.  You plug a PC into one socket, and a plastic case battery charger into the other.  Unbeknownst to you, the battery charger has a hot-ground fault.  Ok, so the fault voltage is carried to the ground wire, and is safely grounded back to the panel, right?  No, it's not.  It lifts the ground wire, and thenunction box up to 120V.  Wait, isn't the PC also grounded there?  Yes, it is.  The chassis of the PC is also lifted to 120V.  You touch the PC and blammo.  

The PC does not have any problems.  It got electrified because of the ground fault over on the heater.  In effect, your ”isolated island” of grounding worked against you - it assured that if one device has a ground fault, everything has a ground fault. 

The upshot is, "no half measures".  Grounds start at the link between the grounding rod /water pipe and the main panel neutral ground bond.  Then grounds propagate from there.  Anything else isn't really grounded.