If I remember correctly (it really has been a long time since I used amiweb2c), then its version of iniTeX and TeX is somewhere around 3.1415 instead of 3.141592. But these differences are exceedingly minor and won't affect your normal day-to-day work. What you definitely would need to upgrade is the core set of macro packages, in particular LaTeX2e. LaTeX3 is still under development (to be expected with such a masochistic underlying language). You can find those packages on the Comprehensive TeX Archive Network at, for example, tug.ctan.org. They come with detailed installation instructions; if you have problems, ask around on the Usenet newsgroup comp.text.tex.
I regret I cannot offer more specific advice, since it has been a long time since I delved into the internals of a full TeX installation---ever since I started using LyX (unfortunately not available for Amigas, but is for Unix/Linux, Windows and Mac) I have not looked back.
