Very nice. A few observations:
* Well done, nice project, pleased you completed it.
* Nice you got the cart slot at the rear, good.
* No bowing on the plastic, good.
* A bit thick, ho hum; fine though as I imagine the screen will wobble if you use the system with the built in controls?
* Did you put a switch on the data (white) cable for the controller 1 port (leftmost) so you can plug an external controller in and use that instead of the built-in system?
* Expansion pack or Jumper pack??
* Only 2400mAh battery? Rechargeable inside case? Is it secured in the case with hot glue?
* "C" buttons not equidistant from each other.
* Heatsinks but no fan and airholes? Not a good idea, takes away point of heatsinks and your system might get hot as the heat can't escape. I presume there is a fan in there (I hope).
* Right "C" button recessed a bit much??
* How about using the hinges from the PSone screen instead of regular hinges? (spring loaded)...
* Start button a bit wonky (easy to fix).
* Up button on "C", as you mention.
* No love for D-pad??
* I presume you have left shoulder, right shoulder and "Z" buttons?
* How about screwposts instead of the hinge? Being able to get to the guts is the important thing as things will go wrong, however be optimistic!
* Use some filler to fill in the holes made for the PSone screen controls (in slightly wrong places I notice, and the surplus one by the right hinge.
* Lightly sand the edges to make it look better.
* Like my projects, with the perspex clear, everything looks a mess; consider painting the system and/or cover with thick paper. If you are going to paint, use some PVA glue or similar to stick thin paper to the area before painting, so the paint can have something to stick to; and varnish the paint when done.
* I discovered that perspex scratches very easily indeed, so be careful handling your screen area - not such an issue as the screen closes when the system isn't being used so will be protected anyway.
* Nice big speakers, you will now appreciate why I use them!
These are all positive and constructive points.
I like your system and the work you have put into it. Welcome to the "club" fellow modder!!

This is one of the better N64p's out there - if you paint the system it will look miles better!!
BTW - thanks for the "thanks", appreciated. If I can help in any other way, please let me know.