By specifying -t 4 in the bwa command line, you are telling bwa to use 4 threads. Now, each of those threads will not neccessary max out a CPU, because at any one time, each thread might be waiting for data from disk, or waiting for another thread to finish what it is doing to provide it with the information it needs.

If you want bwa to use more CPU at once, you need to increase the number of threads it is allocated by using a higher number than 4 in your -t option. However, be aware that generally there is a point of dimishing returns on allocating more an more threads to a single task, where adding more threads doesn't help becuase you are bottlenecked by something else.

bwa will use the memory it uses - in the case of batch linux apps like this, allocating more or less memory makes no difference to speed as long as memory is sufficient that there is no swapping to disk (large linux servers usually have disk swapping disabled anyway).

However, the best way to speed this up would be to run multiple instances of bwa at once. At the moment you are running on one fastq, waiting for that to finish, and then running on the next. You would improve things by running 4 or 5 instances at once. You can do this with the parallel tool https://www.gnu.org/software/parallel/.