So are you planning to build a special kernel for these users?
Okay, so based on your answers I guess that you are following the book step-by-step. If that is so, then your permissions issue is most likely that (1) you are logged in as user lfs, (2) your root filesystem right now is the Kubuntu boot volume, (3) you are build on a directory named 'lfs' or a separately mounted filesystem under mountpoint 'lfs'.
Don't take the book literally (I'm afraid that is so). If you are logged in as user lfs you will not have permission to create a directory '/tools'. You should be creating '/lfs/tools' and you need to either give that directory on the command line or use a $PATH variable (which is the same thing).
The 'tools' directory should be created in your build area. That is why you have a permissions error.
---------- Post updated 05-08-17 at 04:17 PM ---------- Previous update was 04-08-17 at 07:25 PM ----------
If your target users are chemists and other scientists have you looked at Scientific Linux?
Scientific Linux
Do you need a kernel to behave differently (eg, bespoke security behaviour or fitting of a back door)? That's why we build our own kernels. If it's just scientific functionality that you want, you may be able to avoid having to build your own.