Welcome, @Alasdair_T
The job runtimes are fixed at UseGalaxy.org. That is for practical reasons at this public site and doesn’t by itself mean there is anything going wrong.
For really long running jobs, you can try at UseGalaxy.eu instead. Jobs will run there until they complete, or fail, or may never die for a really long time due to some problem with the query, or for asking the tool to do something it simply can’t (anywhere, not just on public Galaxy clusters!).
So, you can certainly try and see what happens. But maybe check your MAF content… and the query species term to make sure more is not going on. You can also share your history here for feedback if wanted. 
ps: I love those tools, too! Protocol 5 in our Using Galaxy to Perform Large-Scale Interactive Data Analyses (2012) walks through an example. Most should still be about the same, and you can ask me here about any of that content and the updated usage (first author 
).
Hope this helps!