Installing Ubuntu Jaunty on AMD64 machine

Yes, I only found out during the install that I was dealing with a 64-but box during the install when I started getting architecture errors.
Another unexpected thing was that the i386 version of Ubuntu 9.04 came to 722 MB and wouldn't fit on a 700 MB CD. Not only did I not have any writable DVDs, but ISO-recorder that I'd been using to burn CDs in Windows doesn't handle DVD burning in Windows XP. So, I'm discovering once again why I hate Windows.
Nevertheless, another free app exists which does the same thing and includes DVD burning in XP.
However, the AMD64 version of Ubuntu Jaunty iso weighs in at 696 MB so it fits the CD without problems.
Installation was problem-free and I could boot easily to both Ubuntu and Windows from the resulting boot menu.
However, I did have three problems which I'll list:
1. The LG Flatron monitor which works fine in Windows shows some intense flickering on both sides of the screen in Ubuntu. I was able to eliminate this by reducing the Horizontal Sync and Vertical Refresh rates below (60-70, 55-65 respectively. However, startup became more compluicated as I had to wade through a number of X server error screen before finally the Ubuntu login screen appeared. This problem has yet to be fully resolved.
2. The SiS AGP31 video card doesn't support 3D effects so a lot of the stuff that has become an integral part of Ubuntu is unavailable.
3. I tried to send a small file using woof to the AMD64 computer in Ubuntu. Although, the available file was recognized when I browsed to the server address, it wouldn't download although I tried it quite a number of times.
However, I could readily download the same file on another Windows computer and even in Windows XP on the same machine. This one is very difficult to understand and googling didn't show up very much to help.
Another less serious problem is the difficulty in finding apps that conform to AMD64 architecture. In particular, I had problems finding AMD64 versions of Opera 10 and Chromium browser but they eventually turned up.
Additionally, although fancy 3D docks such as AWN or Kiba-Dock were unusable, I did install Cairo-Dock which works without a compositor. This dock is really not too bad at all.