First, which gryphon did you get?
The monochrome gryphon uses a PHP program called pegasus, it can be downloaded from the PHP website and might also come on a CD with the programmer. The CS and CTS still use the Edge software Fusion.
The process you have is pretty close, I'll clarify though.
For the monochrome gryphon you get the programmer, get your hex code, send in your hex code then wait until they write the tune. Then when they tell you it is done you use Pegasus to load the custom tune on the programmer.
For the CS and CTS you get the programmer, get and send your hex code, you get a notification to update your programmer, after you update your programmer you reply that is is updated, PHP puts the tune on Edge's Fusion server where you do another update. After that you keep the programmer in your truck.
As for which tunes you replace and which ones you get you'll have to look at your invoice. 87 custom performance tunes usually replace the level 1 transmission tune because that tune is rather useless for anything besides basic diagnostics. A custom tow tune usually replaces the canned tow tune because you really only need one tow tune on a gas truck.
Now for time, I can't say. That depends on how crazy it is in the office. I know back when I ordered mine I just forgot about the custom tune that I ordered so the wait wouldn't seem long...it actually worked very well and was a nice little surprise.
