Playing the Portugese. Their boat does not appear in the Europe screen. Instead a large pink rectangle is visible (I'm guessing the art file couldn't be found)

Correct. There's a little zip file floating around (on the download thread I think) with the Portuguese and Dutch ships for the Europe screen. :)

I can't exactly find where this bug fix is at. I assume this fix will be included in 1.06.

When can we look forward to more options for civs in future versions. I'm partial to Russia and Denmark.

I can't exactly find where this bug fix is at. I assume this fix will be included in 1.06.

When can we look forward to more options for civs in future versions. I'm partial to Russia and Denmark.

New civs will start appear from about 1.09 after more core work is done. :)

Another bug. I founded a city on the Pacific and set up a trade route for my carrack to Europe. However rather than using the Pacific (four tiles away), my ship travelled all the way to the Atlantic before heading to Europe.

I think this could be solved by defining the sea areas as "Europe via West" and "Europe via East" and then enabling the relevant areas in Jeckels trade screens.

An easier way is to just move it onto the pacific ocean tiles ;).

I can't exactly find where this bug fix is at. I assume this fix will be included in 1.06.(...)

See here (post # 498 of the main thread of AODII) to get the file and instructions where to put it:

http://forums.civfanatics.com/showthread.php?t=292143&page=13