The basics: Project/Sequence settings should exactly match your source footage. If necessary, use that Desktop Project Preset, and adjust as you have done. The adjustments just need to match that source footage perfectly.
Now, with mixed Assets, such as you have, one has to define what is the most important, or oft used format and its specs. That is what one chooses for the Project/Sequence Preset. Then, they either convert, or manipulate the other Assets to match that. For stills, Scale to match in Photoshop. For Flash, Export to the appropriate specs. from the Flash program. This will be the same general workflow for all odd Assets, and you may need to use a conversion program on odd AV Assets. Do not Scale in PrPro, unless you cannot help doing so, say for animating Effect>Motion>Scale with Keyframes, etc.
This will give you the ultimate editing experience and the highest quality.
Now, when it comes times to Export, just consider you delivery scheme and the required format. This is not a consideration, when doing the initial Project/Sequence Preset. It only comes into play on Export.
The one exception would be if you have SD material, but know that you need to end up with HD. Then, you would first convert all of your SD Assets to HD with a product like Red Giant's Magic Bullet InstantHD, or similar, and Import those converted Assets into an HD Project/Sequence. That would still get you a Preset that matches your new source footage perfectly. It only introduces an intermediate step at the beginning of the workflow, prior to choosing a Project/Sequence Preset.