I'm doing the exact same job right now. My pump was working fine, but I decided to replace it while I was replacing all my fuel and coolant hoses. I figured it would be a 30 minute job, but it's not the most accessible thing. It came out pretty quick, but I failed trying to get the new one installed today. I actually ran out of time and had to quit, but I couldn't get the bolts started after trying for at least 20 minutes. I think the angle on the threaded fitting might be slightly different compared to the old pump and that's making it tough to line up. Or maybe I bent the hard line a little removing it. Regardless, I won't have a chance to try again until Sunday, hopefully the next try will go better. I may remove the fender liner to make access easier. I also thought about removing that metal coolant pipe section. I'm hoping the push rod stays stuck in place until Sunday. One tip for others doing this - I'm pretty sure the fuel pump rod is furthest in when the engine is top dead center. I spun the engine around a couple times to make sure I had the rod all the way in. Remember that the rod rides on the cam (not the crank), so you can't just go off the timing mark on the harmonic balancer. The rod will either be all the way out or all the way in when that timing mark is alinged, it's pretty easy to feel the difference.
I noticed the same different between pumps and I bought mine from Mac as well. My 2009 rebuild is also a melton. I've notice a couple small sloppy things with the assembly, but nothing too bad. It did have cracking/leaking injector return lines when I got it, so they cheaped out on those hoses. All the other rubber on the engine was good, but I'm replacing hoses since I consider it cheap insurance on hoses that has been sitting for 13 years. I think all the hoses combined were less expensive than the actual coolant.