If your pony to customise is fairly common, and has nasty knotted, frizzed hair, then this is a good starting point.

Take the pony's head off and clean her thoroughly inside and out.
To save time, cleaning is much quicker using an electric toothbrush!

If the head is really stubborn (e.g. post-1991 or harder plastic MLPs), use strong sewing cotton soaked in nailpolish remover.
Hold it as if it's dental floss and work at the neck seam in a sawing motion.

If you are going to add new hair, make sure you take out all the old stuff.

Make sure to do a thorough job, as sometimes bits of hair and glue get stuck underneath the row of holes where the hair was originally sewn in.

Prepare painting materials :-

acrylic inks (the type in the "eyedropper" bottles are easiest to work with)
fabric PVa medium (to use with paint)
mixing bowls/pallete for paint
brushes(make sure to find tiny ones for fine detail)
cocktail sticks/toothpicks(for VERY fine detail)
old newspaper to work on (to protect against paint spills)
paper towels (to wipe brushes, etc)
clingfilm, masking fluid/film, masking tape (for masking)
air/water soluble pen (optional - for rough marking)

To get the head and body ready for painting, I find some small bottles that will fit the neck-hole and put cling film
over them before sticking the head/body on the end. This gives a stable base to paint on and for drying purposes.
If you can't find a small enough bottle, stick the pony head/body on a pen or pencil, and rest it in a bottle.

I tend to apply latex masking fluid (using a cocktail stick) over the eyes so that I don't need to repaint them later.

If you want to paint the entire body, using an airbrush and acrylic inks gives a good finish.
Remember not to hold the airbrush too close to the pony, as this may make the paint blotch.
You can use a paint brush, but the airbrush gives a more even finish.

When you are happy with the paintwork, peel off the eye masking and use a paintbrush to tidy up edges the airbrush missed.

IMPORTANT NOTE: if you are not airbrushing before applying symbol, spray varnish the plain pony before you start,
as this may prevent the paint "bleeding" over time, and protect your artwork.

Suitable hair (from "donor" pony, or hair extension hair)
Long-nosed pliers
Very small rubber band or cotton, to secure tail hair bundle
Plastic-coated wire fastener
Scissors
Needle & thread
"Fray Check" (a haberdashery item, used for fabric neatening)
Old newspaper or similar to work over
Infinite time and patience ;)

Prepare some mane sections. Cut hair sections double the length you
need, with enough strands to fill a plug when the length is doubled over.

Fold the length in half and double-knot at the top, leaving 5mm or so
free at thetop to allow for slippage.
For curly doll hair, or if you only have short pieces to use, tie
the bundle of hair at the top without folding in half first).

Secure the knot with a *small* blob of Fray-check liquid, this will help
keep the knot secure. Not essential, but handy!

Get a length of sewing thread and a needle ready.

Fold the thread in half lengthways and thread BOTH loose ends
through the eye of the needle at the same time.

Push the needle from the outside of the head, through a hair
plug hole, through the neck so it pokes through the neck hole.

With help from the pliers if needed, gently pull the thread
through so the LOOP end is at the neack an the 2 LOOSE ENDS
are at the top/outside of the head.

You can use a loop of jewellery wire instead of needle and thread, but
you need a supply of wire (breaks occasionally)and it's not recommended
if the whole body has been painted.
This is because it flakes the paint the hair's pulled through).

Catch the loose end of your hair bundle in the thread loop and pull!
You can pull through two small "bunches" of hair at a time this way,
which is about all you need to fill each hair hole

Repeat until all plugs are filled. You may need to do each several times
if you cannot pull enough hair through at once.

This may result in much time used, many broken lengths of thread and
various amounts of screaming.
A nice long film is recommended to thread hair to.
Buffy episodes work equally well.

For the tail, cut section of hair double the length of the tail-base to
tail-tip (using an actual pony's tail for reference is useful to gauge length
and thickness required.

Secure with a tiny elastic band or tightly tied thread at mid-point of tail.

Get a plastic-coated narrow flexible wire (the type that hold toys or
electrical goods into their packaging).

Bend wire in half and place over central part of tail.

Use the wire to thread the tail into the body from the OUTSIDE IN.

Make sure you don't have too little or too much hair in the bundle or you'll
end up with a skinny tail, or a mass of hair that won't fit in, and may damage
the paint if the whole body has been painted.

Pull as far as you can and bend over the wire, twist as neccessary
to secure.

You could use a tail washer as found on ponies originally, but this method
works easily and you don't end up with rusty washer problems

Pull tail back to its correct position.

You can also use these hair rooting steps when restoring ponies, rather than customising.

You may need to tidy off paint chips around mane/tail if neccessary;
try to blend this carefully with the paintwork!

Congratulations - hopefully, you should now have finished your custom pony!