We have a somewhat unique service set up at a bank/post office. 500kcmil fed from utility pole mount xfmrs to trough and two meters on exterior wall. 500's go through trough and feed a 400a 3p 4 wire meter, than into buiding to disconnecting means. 3/0 is tapped off of 500's in trough to feed a 200a 3P 4w meter than travels inside to disconnecting means.

I would like to pull 500's out of trough (line side of meters) repace trough with 24x20 nema3 box. splice onto the 500s and go to my new 400a disconnect, which will than feed transfer switch. Than from transfer switch, come back to nema 3 box and feed meters. Is this legal?

Why not get a Service rated transfer switch , go from Tap to meter, Meter to Transfer switch, Transfer switch to service rated Disconnect Switch.
I think the Power Company won't be to happy about having a Transfer switch ahead of the metering.
You also can't mix Service conductors & Conductors after the Service disconnect(feeder) together.(230.7)2005 NEC in the same conduit or J box.

It does not sound like it is a good design.
Every time the genset kicks on and provides power it will go through the meter and the customers gets charged for it?

It may be best to consult with the local POCO.

The service-rated transfer switch should only ever go downstream from the meter, not upstream of it.

If you want both services to be on generator, you would need to get two transfer switches. One generator can feed multiple transfer switches, you just have to be careful about what you do with the neutrals when you're dealing with multiple services like that.

You can also buy CT metering units. That meter it after utility meterting if you want to know power usuage, There used all the time in office building with several tendent but only one utility co. Main meter.