Hi Scott,
I think you're absolutely right to work on your timing some more
That's the one thing that most Aikido students really struggle with, and yes you do need a middle gear, and a slow-middle, and a fast-middle, and the ability to change speed (particularly as uke) mid-technique!
As for true and honest attacks, are you attacking from your centre? If you are then no problem, you are being honest
It's just a case of sorting out your speed to be appropriate for the level of the tori you are working with...
You are on the right track, keep it up!
Ruth