Lowering the saddle can have an impact on tone because the angle at which the strings break over the saddle is reduced, therefore downwards pressure on the saddle is reduced.
That guitar has arrived in Johannesburg in winter from... wherever it came from. Jo'burg in the winter is very dry, and I'd expect that to have an effect on a solid top guitar. However, usually the consequence of the wood drying out is that the top goes slightly concave, the bridge drops and the action gets low.
It's not necessarily the bridge. Could be the nut. Could be the truss-rod.
Note
1) Try playing the guitar capoed at the first fret. If things get a lot easier then start suspecting the nut
2) The truss rod effects action but that it is not it's primary purpose. If the neck relief is not correct then by all means use the truss rod. However if the neck relief is OK and the action is still a problem then resist the urge to flatten out the neck to lower the action - all you will do is create a different problem.
If you saved big money then take a little of what you've saved and have it set up properly. Phone around for prices or take it into a shop for them to have a look at. BE SURE YOU UNDERSTAND WHAT YOU ARE GETTING - EG are they going to polish frets? If they tune the nut is that going to cost you more? Remember it's not a guitar you bought from them so they don't owe you any favours.
Simply sanding down the saddle because the action is high is not the way to go. Figure out what the problem is first. It MAY be the saddle, but it's not a given.
If you suspect the nut then take it to somebody who knows what they're doing. I tweak truss rods from time to time, I might even sand down a saddle (if I have a suitably flat surface) but the nut? No way, Jose. Nuts I leave to the experts.
See
http://www.frets.com/FRETSPages/Musician/GenSetup/TrussRods/TrussRodAdj/tradj.html for some helpful notes on checking and setting neck relief.
See
http://www.frets.com/FRETSPages/Musician/GenSetup/NutAction/nutaction.html for checking the nut.
Maybe the 12s are just more than you can stand. I know a guy who has 9s on his acoustic ? He finds my guitars (strung with 13s) unplayable.