I will really like to show you exactly what to do to get rid of the pops with what you use but I need to know all hardware and software involved.
I will assume you most likely do not have a standard wordclock standalone sync master like a Big Ben.
I will assume again you are using Pro Tools so in Pro Tools you need to set your clock sync to ADAT and not Internal.
making sure that both systems are using the same Sample Rate and Bit depth.
Example:44.100 16 Bit, 48.000 24 bit.
You should never normalize Its bad for the Audio in mine and most of the professional engineers I know opinion.
This has been tested and is just not a good thing to do for your MPC 4000
sequences or audio in general unless you really know what you are doing.
"Louder is not always better" I know you make think it sounds good but that's just a hearing illution because you proably like to blast the speakers
If you want a clean punch from your MPC to Pro Tools make sure to use good converters and set the level at Middle this way you wont clip and you will leave headroom for plugins and FX.
Need a pic let me know.