I have just baught my first 79 stanza it's running a 4 speed L16 I have an L20B laying round and was woundering how hard it is to swap them around as far as I can tell it's all similar what are the major changes I have to make to get it in??

It should drop straight in and bolt up to the gear box and cross member, may have to swap the sump

use the stanza sump (use a new gasket and gasket cement)
use the stanza engine mounts.
Maybe change the alternator (only required if the stanza one is internally regulated and the l20 externally or vice versa)

everything else should be a straight swap

I have been told I need the sump and oil pick up so it will fit over the stanza cross member??

yes mate that's correct.

Also exhaust will sit 20mm higher might be an issue

make sure the flywheel is with the L20(6bolt) as the L16 is a 5 bolt

Just check the sumps aren't the same before swapping them!!
I didn't need to with my s1 bb into 78 stanza swap.
Then check
Flywheel
Engine mounts
Exhaust

It's pretty easy but there's some fiddlybits to work through

What's the best swap for the gear box wanting a 5 speed over the 4 speed that's in it and I would like to get away with not cutting anything if I have to??

Some stanza's had a 5speed from factory with reverse over first gear. This would be your best bet. This is a short box. A stronger but more expensive short box would be an R30 Skyline but these are often grabbed by 1200 ute guys with Ca18's so are harder to find.
This info is all over the forum if you search a little...

Just want to say thanks for all the help everything that a you all have said has been spot...