Hi,
Big performance issue with your configuration.
To explain, install is incremental, so all is done as if you successively install each version, one after another.
To have an idea, on my hosting server, full install is about 20-30 seconds.
I also have a laptop (i7, SSD drives, where install is about 30 seconds)
I recently bought a desktop (i7, HDD) : install was about 4 mn

: I could see that mySql used 100% HDD activity

((
I solved issue moving data files to another HDD (small SSD of 20GB) : install is now 15 s
So :
1) check your HDD : maybe cache is not conrrectly used or else
2) check your MySql config : try and use cache as much as possible, configure host as "127.0.0.1" (avoid "locahost" which can lead to bad DNS perfs)
3) sometimes, disabling IPV6 can help (I found this trick on the net, but it did not work for me)
4) if you have possibility, try to set data to another drive
As a workaround, try an incremental install.
As far as I could seeon you logs, setup ran up to V3.2.0, so for instance, you could try fresh install (new database, new setup):
1) install V2.0.0
2) upgrade to V4.0.0
3) upgrade to V5.0.3
This is only a workaround, but it should work in your case, in case you don't find how to fix perfs issue.
To notice, in my case, after correct install, even with long setup, use of application is correct (but even better when perfs issues are fixed)