Gee, I haven't had any problems at all loading 9mm. However having learned the "hard way" that trying to combine Seating and Crimping is not worth the hassle I seat and crimp every single caliber I reload using separate stages for these critical steps.
To DIY guy, I have to question a statements in your original post.
The instructions I've found for proper setup all seem to go with the Custom die which has three parts and the American only has two.
This implies that your Hornady American die set only came with 2 dies. Looking on the Net indicates that the Hornady American dies set for the 9mm has a full length Sizing/Decapping die, a Flaring die, and a combined Seat and Taper Crimp die. Along with that you should have also received a shell holder for hte 9mm. Hopefully I am mis interpreting that statement of yours and you actually did receive all of the parts necessary for a complete die set.
Now, typical procedure for a 3 die set is to size and decap in the first operation, then flare the cases in the next operation, and finally seat and crimp in the last operation. As I stated I am NOT a proponent of combined seating and crimping and will tell you that you can use your third die to seat and crimp in separate operations by re-adjusting the die so it just does one operation at a time.
Now a run through on typical setup for these different stages.
First, you have to set up the Sizing/Decapping die. Something that is VERY easy to do for a handgun caliber like the 9mm. Typically you are supposed to bring the die into contact with the shell holder and then back it off by 1/2 to 3/4 turn. The easy way to do this is to place the shell holder in the ram on your press, raise the ram up with the shell holder empty, and then screw in the die until you feel it bind up due to contact with the shell holder. At this point put a dot on your die with a Sharpie pen at the 12 o'clock position. Now lower the ram and rotate that die 180 degrees Counter Clockwise so that dot is now at 6 O'clock. Then hold the die in position and bring the lock nut down and snug it up tight to "lock" the die in place. Then get out your hex key and and tighten the locking screw on the lock nut. At this point you have your sizing die set.
Next step is to adjust the flaring die, a setup that can get a lot of newbies in trouble. The way I like to set up the flaring die is to insert a sized case in the shell holder and then bring the ram all the way up. Then I start screwing down the flare die until I feel it starting to bind in the case. Then put a dot at 12 O'clock on the die with a Sharpie and lower the ram. Now, depending on the brand and the specific design of the flaring die you can typically have something in the range of 3 to 5 full turns of the die before it starts forming at actual flare. So I start turning the die in and counting. I'll go in 1 turn, cycle the ram up and down and then look for a flare. I keep on going in 1 turn at a time until I can actually feel the press working the case and producing a visible flare. Very often a result of this particular coarse adjustment is a very large flare but it allows you to narrow down the actual "working window" for the flaring operation. If the flare is giant, then back off a half turn and see what happens with a fresh case. The goal for your flare is to get the flare to the point where a new bullet will go into the flared case by 1/32 -1/16 inch and NO MORE under simple finger pressure. Once you have your die adjusted to this point draw a line on your die with your Sharpie at the 12 O'Clock position. Then tighten up the lock nut and re-check the flare with a fresh case. Note, many times you'll have to turn the die in just a smidgen because tightening that lock nut will actually draw the die up slightly in the thread of the press due to the clearances between the die and press threads. So if you need to tweak it a bit that's totally normal. BTW, once I have everything cast iron dialed in I use a diamond burr in a dremel to mark the 12 O'clock position of my dies.
Finally setting a Seat/Crimp die for just seating the bullet. What you do here is turn the bullet stem in by 3 or 4 full turns. Doing this will allow you to seat a bullet without the crimp ring ever contacting the die. Note, you will want to make note of the number of turns on the bullet stem you use between stages and be consistent about it. I'll also note that you could purchase a Lee Factory Crimp Die for 9mm and avoid having to re-adjust your seating die. Once you have the bullet stem set and locked in you then need to slowly bring the die down until you have your desired overall length. Then set and lock in the lock nut. At this point a couple of scribe marks on the lock nut and corresponding marks in the thread just above those scribe marks can make finding this position of the lock nut much easier.
Finally setting up to Crimp only. Start by backing out the bullet stem 6 full turns to insure it won't contact your bullet during the crimp operation. Then loosen the lock nut and run it up the threads on the die by 5 or 6 full turns. Take a case with a bullet pressed in place and put it in the shell holder and raise the ram. Then take you now Crimp die and screw it down until you feel it contact the case. After that point it will only take something in the range of 1/2 to 1 turn more to crimp your bullet in place. Note, I use digital mikes right at the very edge of the case to measure the diameter at the crimp. Then I'll take a measurement about 1/8 inch further down. When I set a taper crimp I set it to be 0.002 to 0.003 inches smaller than the diameter of the case where the bullet is sitting. While that doesn't seem like much of a crimp it's always worked perfectly for me.
Finally a note about overall length.
First, use a length that matches the profile and weight of the bullet being used
as listed in your load data. DO NOT use something that "matches" a commercal load from a maker such as Federal. Because they will NOT be using the powder you are loading with. Use the length provided by your powder manufacturer, it's a very important detail. However, a deviation of only 0.005 inch is not a big deal, so if your length is within 0.005 inch you really don't have to fuss to get it spot on perfect. Also note that is just 5 thousandths, NOT 50 thousandths. Please, count the zeros because that can be critical.
Second, profiles between brands are typically quite close in overall lengths, so if you are using a Rainier RN bullet it will be within a few thousandths of a Berry's or Extreme RN bullet. However between a 124 grain FP bullet and a 124 grain RN bullet you may find a rather large deviation. Personally because the 9mm has always used a Round Nose bullet profile I've never tried one of the newer Flat Point plated 9mm bullets. Because finding load data for these oddballs can be difficult and I don't have any need for a 9mm FP plated bullet load. However if I did want to try out one of these bullets I would start by purchasing some 9mm Hornady XTP's because those are typically FP profile bullets. Then I would compare the length of the XTP to the length of the plated FP I was considering and adjust my overall length as needed to have the base of the bullet in the same spot as an XTP base would be. Because data for the Hornady XTP is very easy to find. I'll also note that I have found Hornady XTP's to be superbly accurate bullets.
Anyhow, this is how I set my dies up and I haven't had any problems at all doing it this way. I will also note that I have a Lee Factory Crimp die for every caliber I load, Rifle and Handgun. Some don't like the extra sizing ring in the handgun dies but I have never had any of the supposed problems these sizing rings might cause and they do insure every assembled round will chamber properly.
