What regulations apply to a VFR flight from South Africa to Namibia? I just would like to know what kind of flight plan, permissions, en route airway paths and other factors that need to be considered?

Other than the passport, PPL license and aircraft documentation and so forth.
For SA to Namibia:
Factors to consider

Buying all the appropriate charts.
Clouds: if you can't maintain the required separation, you need to switch to IFR, which means the plane needs to be IFR-equipped, and for you to be IFR rated.

Sources: Namibia AIP GEN 3.2 and ENR 1.2

En route airway paths
All airways from SA to Namibia are Class A, so VFR is not allowed along ATS routes.
Source: Namibia AIP ENR 3

Permission
You need overflight permission from Namibia, else there's an up to N\$50,000 fine or 5 years imprisonment. It is submitted 24 hours before.
Source: SA AIC D 012/2014

Flight plan – yes
Across international borders flights do require flight plans (the ICAO type) in accordance with ICAO SARPs Annex 2 (Rules of the Air), which both SA and Namibia require.
Sources: SA and Namibia AIPs GEN 1.2

See also:

SA AIP
Namibia AIP


For any other countries that share a border, refer to the respective AIPs.