You need to move to ETrade, the money is available for investment immediately, sometimes my checking account is low on funds and before I transfer money into it I'll make a transfer on ETRADE and it lets me trade in seconds before checking if the funds are available.
If you call them(Scottrade) and ask to waive the 3 day wait they will, always do for me(just have to make the bid on the phone). Also you can ask them to waive commissions on penny stocks and pay a flat fee. I called and told them I would be switching to TD if they could not match their flat rate fee on pennies and they did.