'Llith' does mean lesson as in gwers, article or lecture, however, it is used more to describe lectures-the modern noun for lecture is 'darlith' where 'llith' is incorporated into the word. Also, the modern noun for article used is 'erthygl' so I'm not sure whether 'llith' is archaic or not. I've not come across is apart from 'darlith'.
There is no real interchange between the words 'llith' and 'gwers' because they mean slightly different things.
As for the use of 'gwers' for verse, you're correct Beith, it does mean lesson and/or verse. However, other words used for verse are 'adnod', 'pennill' and for describing the whole verse as poetry: 'barddoniaeth'. ('Bardd' for poet

) For describing a verse in a poem I use pennill as it's the noun most commonly used! Probably to avoid confusion with 'gwers' as in lesson. All depends on preference and dialect I suppose.
As for the word 'gwersau' I've never come across it, in conversation, school or the dictionary! I've looked on the internet but the sources who have used 'gwersau' are mostly Welsh learners blogs and stuff. I have found in my dictionary, 'Gwersebau' which is plural for doctrines. Otherwise I'm very tempted to say it's a grammatical mistake. I can't be 100% sure though because I can't vouch for others!! (I'm South Walian). I found nothing whatsoever for 'gwersoedd' :S
What geiriadur are you using Neeltje? Is it the Geiriadur Mawr? Or the Modern Welsh Dictionary? That might make a difference.
Welsh is an ever evolving language-aswell as very complicated! There are often many different words for one thing and then those words are sometimes used elsewhere for different things! To cater for this, the words previously used become more archaic in the original sense but when used for the new thing it's perfectly fine. lol. And then there are the dialects....
I hope I've helped somewhat. I'm sorry I can't give the in's and out's of why and how and the linguistics as I've grown up speaking it and can't remember learning it (if that makes sense).
~*Efo can yn fy ysbryd,a'r heniaeth yn fy ngwaed,rwy'n byw bywyd llawn efo calon Celtaidd*~