As far as I know, you can use a standard RNA-seq pipleline and the tools you mention seem fine. This assumes that the reads are not too short to map (~25 bases minimum). I am not sure about the deep sequencing part with the other pipeline … maybe check at a scientific forum where other people using that tool are? Biostars or SeqAnswers is where I would start! You could also ask at the GTN chat – maybe Cristo will see your question (he is who helped in the other topic you asked a question in). Find that chat at the top of the tutorial website.
For the data part, you can get the reference annotation from here. → miRBase - Downloads
Once the GFF3 file is in your history (Upload tool, all defaults), you can convert it to GTF format with gffread. This will make it easier to use some of the tools with default settings, or you can probably use the GFF3 and customize tool settings. By “customize” I mean adjust the attributes that you want tools like FeatureCounts to use for the summaries. These are set for GTF format by default but people use these with GFF3 – just match up the attributes by inspecting your file for the labels used.
And, as an example, I downloaded the human GFF3 into a history here. The data is a match for the built-in UCSC hg38 reference genome at the UseGalaxy servers.
Please have a look and let us know if you have more questions! Happy to see you are following up to tackle this project again! 