is it possible to have a trader tax status and also have long term stock positions subject to a lower capital gains tax rate. must it be held in a separate account?
If held in a separate account, it certainly makes proving it easier. However, if you document each long term stock position appropriately, I believe you can comingle long term positions with your trading account. But for clarity and simplicity, having long term positions in a separate account is ideal.
Traditionally the IRS won't allow you to cherry pick. That's kind of the point of trader status, but you should consult directly with a tax pro. If cherry picking was allowed there would be very little point in the election of trader status.