What I did:

Throughout, I used #6 wood screws & predrilled the holes with a countersink bit.  Since I was driving them into the edge of 5/8" particle board, pre-drilling helped to minimize breakage.  One of many lessons learned from TheQleaner.

First, I assembled the control panel box.  
It was a piece of cake.  I used the jig saw to put a 45degree angle on the back panel of the control panel so it would fit flush against the control panel.  Then I attached the front & back to the base, which fits inside the walls of the box.  Confused?
Then I attached the sides & made sure they fit.  One side was off, so I had to re-cut it from scrap. oh well.  Then I made the cutouts for the trackball & spinner, and set the control panel aside.

Here are some pictures:

The completed control panel box. The Control Panel top in it's raw state.

Then I assembled the cabinet.

It went together pretty well, even though I didn't have a helper at the time.  I made the top & back panels as well as the speaker panel flush to the edge of the sides. The top, angled back, and upper back were cut at 45degree angles along the edge where they meet so they would fit well against each other.  Then I attached the control panel.  
I did all the control panel wiring over the next couple of days & got the cabinet up & running because I just couldn't wait any longer to play some games on this thing.  I printed the big mame logo out & put a blacklight behind it as a temporary marquee while I 'playtested' the cabinet :)
At this point I didn't have a router, so I held off on cutting the grooves for the T molding.  Instead I hunted down black contact paper & used it to coat the exterior surfaces.  It took about 9 rolls ($3 each) to cover the entire cabinet.
Next came the front panel, which would later become the coin door.  I used flush cabinet hinges and mounted it up.  I should have waited.  I failed to account for the t molding when I attached the coin door.  Once the T molding was on I had to reposition the hinges so the door would open.

Later, I borrowed TheQleaner's router & cut the grooves for the t molding.  I had originally planned on putting t molding all around the cabinet, but since I made the front & back panels flush their screws were in the way.  I should have recessed all those panels by a half inch.  I ended up just putting it on the front surfaces, which looks fine since that's all the player sees anyway.

I also added big L brackets under the monitor shelf for extra support, and finally I installed the marquee retainer & Plexiglas.


Finally, I installed a 25" TV for the monitor, printed a new marquee and made a bezel for the monitor.


What I should have done:

Cut & used the base plates.  It would have added more support to the bottom.

Recessed the cabinet top, upper & lower rear panels, angled rear panel, & speaker panel.  It would have allowed me to use T molding all around the sides and the only component who's dimensions would be affected is the plexi in the marquee.

Mounted the coin door AFTER installing the t molding.  No big deal.