First off, a slight bump thru the frog is completely normal.
Watch this video starting at 3:10. Tim explains this very clearly:
http://www.handlaidtrack.com/videos-a/144.htm?video=boUNeUukmZE&title=Installing%20The%20FrogpointsSecondly, and this is just my personal experience thus far (and note i'm using the HO fixtures) I have found a couple things.
Get yourself one of those head band magnifier like this
I have found this helps a lot getting the rail properly aligned on the point/frog form tool in preperation for filing. Note I also use the frog helper tool) Then I use the magnifier when lining up the two halves dead on equal in the frog helper.
Also, it is very important you solder the wing rails very carefully and dont let the solder wick underneath and onto the opposite side where the frog point is going to go. (I've done it) The frog rail will sit on top of the solder and not sit flat on the PC ties. I also am careful to file the frog point flat on the bottom of the rail (Only file enough to knock off any solder, not the rail!) after I solder the frog halves together.
Personally, I have found the most critical thing is to get the wing rails right ESPECIALLY the bend (where they will align with the frog) I spend a lot of time forming the wing rail so it drops in the fixture nearly flawlessly on it's own..NO FORCING! I have also invested in the rail bender tool and this makes the job of forming the diverging route of the wing rails much more consistent and keeps the rail true thru the radius. (This is just me, I never could get a consistent radius by bending it by hand)
Hope it helps.