Not nearly as in-depth as many other customs in here, but...
The main thing I tried to do was make sure the mods didn't prohibit transformation and I wanted to make sure I didn't have paint in any high-rub areas, where transforming him would take paint off.
I did the figure in stages.
The first thing I did was remove the wings. Since they can still be clamped on to him like a shell when he is in gun mode, it meant that the simple mod didn't mean sacrificing his transforming ability, but IMO also greatly improved his overall look in bot mode.
The next thing I did was, use black Rit dye for his purple parts. Chest, lower legs, and lower arms. With a Decepticon sticker from reprolabels.com. Also gave his gun nozzle and scope tip a bath in some Rit too.
This all finished the first stage.
As much as the Classics Megatron's cannon didn't bother me, there was just always something about his original cannon that I have always liked, ever since I was a kid. So since I had an extra original scope/cannon I decided that if I could find a suitable way to mount it, then I would.
At first I thought about modding an original G1 Megatron scope mount and adding that to the figure. Then I came up with a more simple, and cheaper, way to mount it. I had some 1/4" sheet styrene left over from another project. I measured it, cut it out, and then shaved the angles on to the sides. A couple of small screw holes later, and the mount was attached to his arm. I also took this opportunity to mount it on the side of his arm, instead of the bottom. I thought about the top of his arm (G1 accurate) but it would've severely limited his arm poseability and possibly messed with his transforming too.
I then dipped the mount in to some black Rit dye, and it was good to go.
For transformation the original scope can be re-attached and the new cannon can be removed, leaving his original Classics gun mode intact.
The mount (white) can be seen on his arm:
Then in the next stage I used red Rit dye for his mid-arms and to make his light green "light-pipe" head piece and eyes red.
After trying different mild methods of paint removal for the purple on his shoulders, I decided it would be better to just paint over it. Rather than risk gunking up the pale plastic on his shoulders.
I was very pleased that the standard square bottle Testors silver paint not only goes on smooth, but also matches his factory silver face paint perfectly!
I also used the silver paint to cover up the black parts on his inner thighs, and a little semi gloss black to cover up the grey spot on his groin.
All of these paint spots are in out of the way enough areas that they do not rub during posing or transforming.
With Music Label Soundwave:
Eventually I plan to do something about the yellowish-orange bits on his thighs, but I haven't decided what yet.
I really liked the Classics Megatron, but since he was always my favorite character, I couldn't help trying to make him look closer to the version I wanted as a kid (more G1 looking).
_________________
"Now I am somewhere I am not supposed to be,
and I can see things I never really should've seen,
and now I know why, and now I know why...
things aren't as pretty... on the inside"
Matthew – 
I just said a post by Dark Jedi makes sense. I am going ice-skating in Hell tomorrow.