featureCounts will allow you to use multiple files at the same time and will generate a count matrix in one step. It is also much faster and will sort files automatically, if needed.

You can use GNU parallel to run multiple instances. See this tutorial for further information.

A small perl script will do the job and then use R to combine results into one file.

Why not quantify with Salmon - will give you much better gene level estimats (according to amongst other this)