I want to change my front struts. Do I need to seperate the upper balljoint , Or can I remove it without doing so? . And as a rule do you always replace the Strut mount( I believe thats the upper flange) ??? Its a 2005 Tundra 4x4

No need to separate the ball joint. Loosen the 3 top nuts (Not the big center one!). Take the nut of the lower bolt. The easiest way I found to remove the lower bolt is to take a crowbar, rest it on top of the upper A-arm, slip the end of it between the coils and leverage the a-arm down (lifting the coilover slightly) to relieve tension on the lower bolt. Slide the lower bolt out, set the crowbar aside (you'll need it for the install later). Finish removing the 3 top nuts. Hang on tight to the strut as you remove the last nut....it's fairly heavy and can cause pain and distress if dropped.
http://farm4.static.flickr.com/3492/3848572073_632ab0616c.jpg (http://www.flickr.com/photos/jim65wagon/3848572073/)
It's harder to use the crowbar with the Donahoes, but you should get the idea if you can imagine a crowbar on the A-arm.....wish I had a pic of the whole process now.

I'm unsure what you mean by replacing the upper flange. If you mean the top plate with the 3 studs in it; then it depends on you're new strut. Something like the Bilstein 5100s will reuse the top plate from the original coilover. Something like ICONs come with the top plate as part of the unit.

http://farm3.static.flickr.com/2510/3848563409_79561133d0.jpg (http://www.flickr.com/photos/jim65wagon/3848563409/)