Hello Haydon,
I also have a Mach2 and use Sky Safari 6 Plus on an iPhone and iPad to point it. I'm doing this while waiting for the hand controller, so my situation is much like yours. I've had fairly consistent success since late May of this year, but it's been a learning curve. The A-P folks have been helpful. I was among the first to receive a Mach2.

Initially, I had the same problems as you with the Mach2 and Sky Safari: severe disorientation, going the wrong way, and hitting the stops if I tried to use it WITHOUT first initializing it through APCC on a PC connected via the RS 232 cable.

Sky Safari just does not communicate accurately with a Mach2 unless you lay the groundwork through APCC. This may change, but for now, the Mach2 with absolute encoders and the CP5 box is a different animal entirely from the CP4, as far as Sky Safari is concerned. Only once was I able use Sky Safari with the Mach2 mount without the aid of a PC to initialize. I've not been able to repeat it, but I am still trying.

Here is what I do.
1. Make sure the Sky Safari APP on your mobile device is turned OFF. You don't want it trying to communicate with the mount before it is ready.
2. Set the mount manually at Park Position 3.
3. Connect the PC to CP5 via the RS232 cable.
4. Start APCC as a standalone program. It should also boot up with the AP V2 driver. Don't start it through any digital star atlas.
5. Confirm that the mount is connected via the Mount window and the APV2 driver window. You'll see this in the bottom left window.
6. THIS IS THE KEY: Go to the AE tab, and select "set home position". You should get a prompt that will say something like "ARE YOU SURE WANT TO GO HOME" and heck yes you do. These terms my not be exact, my mount is not connected at as I write this.
7. This should synchronize your telescopes actual physical position with "Telescope Position" APCC window at the bottom right.
8. Open the Rate Settings tab and make sure the scope is tracking in the sidereal mode.
9. Open the settings window on your mobile device, select the CP5 Wifi. I've had some trouble here (more on this later).
10. Now you can open the Sky Safari APP and connect the telescope, once your address (172.31.0.1) password, and port (23) have been correctly entered.
11. If properly connected, Sky Safari should show your mount pointing directly at the pole (not polaris). You should be good to go.
12. It is best to keep your scope connected via the PC RS232 cable too. The mount has no problem communicating via RS232 and WIFI at the same time.

some glitches.
1. The CP5 WIFI sometimes vanishes. This is a known glitch. You just need to toggle power off and on. The encoders should know exactly where it is once power is restored.

2. Turn off your cellular data. I find that my iPhone insists on looking for the internet through the CP5 wifi, and when it doesn't happen, it shifts to cellular and ignores the WIFI. Perhaps I'm overlooking a setting here, but this is what I do.

3. Keep your sky safari window active. When I close the window on my phone, or simply go to another open window, the scope disconnects.

4. I've had a few occasions when the APCC program halts the sidereal tracking. You'll know this when a centered target gradually moves away from the crosshairs in SkySafari. Usually, re-aligning the object gets it started again, but you may have to go to the APCC program,
then to the Rate Settings tab, and restart sidereal tracking.

With all this said, please understand that I am new to this as well. The Mach2 is my first A-P product. There may be other ways to do this, and without a doubt, there are many folks out there with far more experience than I.

But gosh, I hope A-P will the keypad hand controller soon.

Best,
Ernie Mastroianni