Just got flash working with iceweasel! Now I just need to sort out firefox, feel like i'm getting somewhere though...

seems you try here - then there - but don't know what to look for...
Debian - and therefore probably Ubuntu - use a command:
update-alternatives
to configure things like this IIRC

Next thing to check:
where are the plugins? Where are the java files and libraries? Same for flash... In which directory did they get installed. Is this directory in your $PATH ?
Does the library-loader know where to find the libraries: look into
/etc/ld.so.conf

That file too is managed by some utility (like "update-alternatives") - but my Debian days are long ago, I don't remember...

OK, got this to work 100% by copying the plugins folder from iceweasel to firefox, I have another problem now. I need to remove iceweasel, apt-get wants to get rid of java though Other than that, things seem to be looking up

I don't know how to prevent a package fom being uninstalled - there are surely several ways.
Java is not just a dependency of iceweasel - it can of course be installed by itself.
If all else fails - reinstall java after it has been removed during iceweasels removal.