The updated Keyboard Maestro version above now adds two options:
- Hide saved searches
- Hide folded and filtered
On speed, the script itself should execute fast.
Marked 2’s webkit technology needs a good amount of resource (it essentially contains a browser) so make sure that RAM is not full of many other programs.
To test the script alone, without Marked 2, temporarily edit out the bundle identifier in the following line, so that the strMarked2 variable name is just bound to an empty string;
//var strMarked2 = "com.brettterpstra.marked2";
var strMarked2 = "";
The script will then simply generate a MultiMarkdown version of the TaskPaper document, and I think you should find that it does that fairly fast.
(If not, you could look in the Console.app logs for anything unusual, and let us know what hardware and OS X version you are using. If the bottleneck appears to be in Marked 2, you could ask for advice on the Marked 2 support forum).