As far as the GI lighting, you can get cool white LED's I forgot which company said they had them for this game ( they are different then normal LEDs). But the insert lighting cant be changed. It's all surface mounted LED's. I saw strobe multiball at TPF and it looked good to me, but I've never seen it on an original AFM in person so I couldn't compare the two.
IMHO I would probably just keep the one you have and throw a color dmd if you haven't already done that, and fix whatever issues yours has to make it perfect and call it a day. You'll be able to customize all your inserts like you like and have the "better" strobe multiball.
Now if you didn't have one that would be a completely different story.