Pepper, I suspect that the 'abrupt' shifts caused by oil-contaminated clutches were causing the traction control to kick in, either as a juddering from the anitlock pumping, or in a total power cut from the engine. I had an event last summer when I thought, for a moment, it was going to let me sit due to a power chop. Since the repair, mine has been fine, but I've only a couple hundred miles on it. I really like so many things about the car, so I hope it stays sorted out.
Among the maddening things about it was the absence of a consistent problem, leading the Ford garage to claim that 'they couldn't replicate the problem.' Whether that was actually the case of if Ford has said to stonewall on it because the problem is so widespread, who knows. It has to be costing them beaucoup bucks to handle the problems, and 'customer service' from the mothership was heavily involved in finally getting it fixed.
'05, the 'inappropriate' gear thing is where my problems first began (the juddery starts and shifts came later as the clutches degraded); the computer controlled shifts reminded you of a rookie driving a standard, and getting caught in too high a gear; to provoke a downshift, your really had to cane it. I have to presume that they did the most recent reflash as part of the work, as the car now seems to be in the right gear nearly all the time, and gentle throttle will give you another gear as necessary. The loaner Focus had its poop together on that score, and now mine does as well; smooth pullouts and shifts.
Full sympathy on liking real manual transmissions; I've a 10 year old Wrangler that I love to drive; I'm the only one in the house who can use it. If the Focus ends up getting traded, I wouldn't be adverse to another manual.