Yes, if you have a Lesotho passport you will be able to visit Japan without a visa for up to 90 days.
The quickest route takes about 21 hours and includes stops in via Johannesburg and Bangkok.
Hopefully, you will be able to visit Japan for at least two weeks because there is a lot to see and do in this beautiful country.
It is advisable to book accommodation in advance as some of the cheaper hotels get fully booked quickly. However, if you do have a problem, there are accommodation booking services at some of the larger airports.
Some of the cheaper and more rural hotels and guest houses will require that you speak Japanese, though bigger, or more central hotels will have English speaking receptionists.
Although it is always good sense to never leave valuables in a hotel room, security is not a problem in Japan.
Have an amazing trip, I have always wanted to visit Japan, please let me know how you enjoy it.