Routing:
I would think a T junction when the line has reached the small board splitting to the two fpga's is no problem.
Just put a series resistor at the driver end (MCP).
For several sockets on a motherboard either use individual traces or resistors at the junction points feeding them to prevent ringing/standing waves.
If you want simplicity and the speed is just a few MHz you can just slow the edge rise time with a larger single resistor value at the driver side.
Routing straight out from one side of the fpga was in reference to the I/O's needed (spi etc). I assumed routed to a pcb edge connector? dimm?
All the I/O's you need are there. Rows 1 and 2 you can route without via's, just traces on the top layer.
Rows 3 and 4 with using vias to the bottom layer. Then you only have to route power, clock and jtag under/across the fpga area.
PCB spec, my suggestions:
trace width/clearance: 0.15mm I don't think there are any factories not capable of 0.15mm today and even home made pcb's with decent equipment can manage it.
Copper thickness, inner/outer layers: 35um This seems like industry standard and it's enough for this board. Sure the thicker the better but if you want more you usually have to pay some extra.
Hole diameter: 0.20mm or 0.30mm Please check with the pcb company about the number of layers you can have and board thickness for each diameter.
Annular ring: as big as possible. Without violating the clearance between the fpga balls.
Even if you have to pay the 0.1mm price, you should make it larger so it's easier to manufacture and more factories can manage it.
0.15mm width/clearance is easy for all PCB manufactures I know of.
0.1mm annular ring and small drill sizes like 0.1 and 0.2mm through thick boards is much harder. or rather this is where there is a larger difference from factory to factory.
Using 0.4mm pads for the fpga should not be a problem. But as I stated previously with our pcb manufacturing clearning house we settled on 0.5mm. 0.45mm is also an option
And if you read about soldermask defined pads for fpga just ignore it. Always use cobber defined and pull the mask away as to not get any on the pad itself.
But not so much as to expose the via/traces between the pads and increase the risk of solder shorts. Check the solder mask precision they specify.