When you say the two lowest gears, are you referring to the two largest (rear) cogs or the two smallest cogs? If the latter, there is a good chance your cable just came loose, and needs to be tightened again at the derailleur, and then everything re-adjusted. If the former, then you definitely have some bizarre binding going on, and if corrosion is not the obvious culprit, pictures would tell the story.
It's not a problem lubing the cable at the brifter, but how do you do it? The housing goes right into the brifter, and the cable is inside of it. You can shoot a little in (assuming Shimano) on the outside of the brifter where the head of the cable sits, but it won't do much. But regardless of where you lubed it, unless it is gunked up galore, it shouldn't be a problem.
The short housing could be an issue if it is obviously kinked.
If you do lube the cables, you should do so only where they are bare and right where they enter or exit housing. At the front end, you should down shift til the chain is in the smallest cog, and then lube the cable (about an inch worth) where it exits the housing at the cable stop on the downtube (or head tube). Shift all the way to the biggest rear cog, and then lube the bare cable (again, an inch or so) where it exits the housing at the cable stop on the chainstay. Also, wipe off the cable lightly after you lube it.
The point of lubing the cable is to keep it moving smoothly in those areas where it encounters friction: that means where it enters or exits cable housing.




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My expertise in bicycles goes back to friction shifters and ball bearings.
Lately I'm more comfortable with throttle and clutch cables (and if those are hanging up, it can kill you 
But, to the best of what I've been able to see without disassembly, the hoods have done their job, and there was neither sand nor salt inside the brifters when I replaced the brake cable housing and swapped my handlebars out recently.
