I think others had trouble answering because there isn’t a good all purpose answer for your question! So, I’m going to try to explain why this is so complicated and we can follow up more with your questions.
A particular tool might “run longer” due to lots of different reasons: size of inputs, content of inputs, how many inputs combined together, core algorithm, parameter choices, cluster resources, and overall server load (when they are sent out to clusters eg the “queue”).
Then, when strings of tools are put together in a workflow, this total timing can vary so widely that it is always more accrurate to just benchmark some of your example samples with your target workflow on your expected server, then estimate from there. One server might be different from another, but I can let you know that most public Galaxy servers will be about the same for work that is processing over a weeks time. Meaning, day to day you might see differences, but those average out. Using collections and a workflow, then getting the jobs queued, is the fastest way to get work processed. Queued jobs still have “a job” – they are holding your place in line waiting for a slot to begin process on one of our largest high-demand clusters. This is really important and why using a workflow is so important for batches of data.
Then for the question about protocol, what you are using sounds like it is what I would suggest. These are those newly created by the IWC → Intergalactic Workflow Commission (example search term “Epigenetics”). The same can be found at any public Galaxy server under the Workflows → Public Workflows tab.
If you want to to explore other choices you can usually search the tool panel with keywords to find other tool choices. Or, if you have a favorite tool found in a publication, you can check to see if it is hosted in Galaxy there, and ask here about analogous tools. You might need to build up your own workflows with these although sometimes the GTN has a training level workflow you can use as a template. Scroll down into the Help section to find these along with examples of how to use the tool in general.
Hope this helps and please let us know if this helps or if you have more questions! 
XRef