Wow, I would've expected the 133MHz ATA/IDE interface would be too fast for an ATmega chip, but it looks like they use it in ATA33 (33MHz) mode, somehow getting it to work with a 4MHz(!) ATmega32.
In this case you shouldn't have any problems with a SATA to IDE converter, since they're designed to support older ATA33 devices.
Note however that the OS SCSI stack is only used for SATA devices. IDE uses a different command set, so you won't see SCSI commands arriving at your ATmega, if that's your intention. (The host PC will certainly issue SCSI commands though, and the SATA to IDE device will translate.)
An alternative that might be easier to achieve is to use a USB interface chip to make your ATmega appear as a USB hard drive. AFAIK this does use the SCSI protocol (perhaps a limited subset of it though), so you would see SCSI commands arriving on your device. Recent PCs can boot off a USB hard drive too, if that's your need for connecting directly to SATA.
This solution would be much less sensitive to timing too, as the USB chip would talk over the USB bus at the correct speeds, allowing you to talk to the chip at whatever speed you can manage.
I'd guess 2 possibilities. The first (and one you should be dealing with anyways) is that you don't have a decoupling capacitor on your flip-flop. You need a 0.1 uF ceramic between V+ and ground, as close to the chip as you can get. Putting it on the breakout board is best, assuming you can without damaging the chip.
The second possibility has to do with your connection to the signal generator. How long is the wire, and how fast are the transitions? If you're not properly terminated and the leads are long, the flip-flop may be responding to ringing on the clock line.
Your connection does not require worrying about timing from input to output. A delay will not make a difference.
Neither of your chips are differential, so I really can't advise you on this issue.
You are handling set and reset lines exactly right.
And while it's a little late, you might consider a different flip-flop. Since you're working with protoboards and are clearly new to the subject, I'd suggest that you get a few 74HC74s in DIP packages. These will simply plug into your protoboard without the need for adapters. For learning how logic chips work, this is a whole lot easier on the eyes and pocketbook that trying to start with little surface mount devices.
Best Answer
Read your error report carefully: it complains about an output, 4.Q, tied to another "output", A:5. The simulator complains because you are likely to drive your input A with some values, but flip-flop four is also quite likely to drive that same exact node with its output. What if A wants to drive a 1 while Q.4 wants to drive a 0? That's not acceptable for a simulator.
So what's the solution? Remove input A. As you see in your above schematich input A is not present. You can preload the counter with the appropriate starting status by driving the PRN/CLRN pins accordingly. You should tie all the CLRNs to something anyway.
Alternatively you can use a selector, or multiplexer: its inputs would be A and Q.4, while you should tie its output to D.1
Of course you will have another input, that is the multiplexer control input: this wire controls what your counter is doing:
Just remember: the compiler is your friend, get used to understand it.