Jamal,
Are you limited to working with the application builder or can you access the source code using flash builder. The application builder will allow you to do a limited amount of configuration but for what you want you may need to delve into the source code.
A trial version of flash builder can be downloaded from here:
https://www.adobe.com/cfusion/tdrc/index.cfm?product=flash_builder
To work with this you will also need the source code for the viewer:
https://github.com/Esri/arcgis-viewer-flex/tags
I have also provided a few links that may help you with each of your wish list, some can be done using widgets developed by others some will require you to play with the source code:
1. The scale text (example: 1:150000)
http://forums.arcgis.com/threads/24407-Show-scale-with-coordinates?highlight=scale+text
2. Identify tool (like the one on the ArcGIS desktop)
http://www.arcgis.com/home/item.html?id=39cf66d58c234279ba728c50461a1a89
3. â??go to xyâ?� (like the one on the ArcGIS desktop)
http://www.arcgis.com/home/item.html?id=edd4a2b7c722493a8b08f53eaa131e1e or the locate widget has similar capability
4. The â??findâ?� tool (done)
http://www.arcgis.com/home/item.html?id=5d4995ccdb99429185dfd8d8fb2a513e
5. Query tool (to choose from drop-down list)
Same as above: http://www.arcgis.com/home/item.html?id=5d4995ccdb99429185dfd8d8fb2a513e
6. â??Findâ?� and â??drop-down listâ?� at the same time: to have the chance to see the available values WHILE typing (the most powerful tools)
http://www.arcgis.com/home/item.html?id=4a61e3e4b0c94300a3a361855d9a344f
7. How to allow moving the layers in the table of contents up and own?
The layer list widget already allows you to do this to services, Robert also has an advanced one: http://www.arcgis.com/home/item.html?id=e2cb71d5c04d40d19e9f945ae0db7ce8
If you want to change the layer order in a map service you need to use dynamic layers:
http://resources.arcgis.com/en/help/flex-api/samples/index.html#//01nq0000006w000000
8. Size of icons is quite small! How can they be enlarged?
If you mean the icons in the header control have a look at this thread:
http://forums.arcgis.com/threads/34685-Modify-Icon-SIZE-of-Widget-that-is-diaplayed-in-the-Header-Co...
Regards
Anthony