The only time I had hesitation starting from first gear was with high mileage on the stock wires..it just sort of started out of nowhere, I noticed it when there was one stoplight going to an interstate onramp I took pretty often and it would always hesitate.
Replaced the wires with nice new Magnecors and it's never hesitated since.
Biggest factor might be your driving style. You want an idle of about 600 RPM, so if you're dropping the clutch and letting the idle below that when starting out in first gear, it's going to stumble. Giving just enough gas by feathering the pedal when letting out the clutch so it only goes up from the 500-600 mark on the tach all the way to the shift point for second. Engine speed usually doesn't go much below 1400-1500 RPM between shifts after that unless something else is wrong.
The IAC moving smoothly is only part of it working. The seals and other stuff inside it can still cause funky operation, usually it will show up in the form of high idle, doing cold idle speeds of 900-1400 RPM even when warm. The higher idle actually helps the shifting out of first gear, though...sort of. Wastes gas like crazy, though.
What plugs/wires? Sometimes using other plugs besides the Motorcraft replacements can cause issues, but again, usually it's an idle thing that shows up when sitting still. Also as mentioned, wires can affect things. Being new means nothing, you can get a bad wire or a set that's just not doing what it should.
My guess would be it's either just how you're driving or perhaps the clutch is going too, giving you a hard time along with the slave cylinder. The whole hydraulic clutch system can be a PITA if any part of it isn't working. Air in the master/slave can throw it off, a tough to push master cyl can make it tricky to let off the clutch smoothly, and a slave that's going makes shifting iffy and downshifting downright fustrating. Add in a worn or slipping clutch with any of those and you've got an adventure.
Beats dealing with the A4LD auto though...or so I hear.
If you're dropping the tranny, it's worth putting in a new fuel filter while you've got all the room you need.