Well I somewhat figured it out. The central global clock multiplexer has some very complicated setup for selecting which signal from the pre-multiplexers is put into the global clock spines.
There are two sets of 6 bits per multiplexer to make the selection. It then depends on the active signal pair on which bits are set.
MC1_S_0 (A)*~(B+C+D+E+F+G+H+I+J+K+L+M) 13 WIRE(VPSPX0) ARCVAL(VPSPX0,HTK0) ARCVAL(VPSPX0,HTK6) ARCVAL(VPSPX0,HTK12) ARCVAL(VPSPX0,HTK18) ARCVAL(VPSPX0,HTK24) ARCVAL(VPSPX0,HTK30) ARCVAL(VPSPX0,HTK0) ARCVAL(VPSPX0,HTK6) ARCVAL(VPSPX0,HTK12) ARCVAL(VPSPX0,HTK18) ARCVAL(VPSPX0,HTK24) ARCVAL(VPSPX0,HTK30)
MC1_S_1 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK1) ARCVAL(VPSPX0,HTK7) ARCVAL(VPSPX0,HTK13) ARCVAL(VPSPX0,HTK19) ARCVAL(VPSPX0,HTK25) ARCVAL(VPSPX0,HTK31) ARCVAL(VPSPX0,HTK1) ARCVAL(VPSPX0,HTK7) ARCVAL(VPSPX0,HTK13) ARCVAL(VPSPX0,HTK19) ARCVAL(VPSPX0,HTK25) ARCVAL(VPSPX0,HTK31)
MC1_S_2 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK2) ARCVAL(VPSPX0,HTK8) ARCVAL(VPSPX0,HTK14) ARCVAL(VPSPX0,HTK20) ARCVAL(VPSPX0,HTK26) ARCVAL(VPSPX0,HTK32) ARCVAL(VPSPX0,HTK2) ARCVAL(VPSPX0,HTK8) ARCVAL(VPSPX0,HTK14) ARCVAL(VPSPX0,HTK20) ARCVAL(VPSPX0,HTK26) ARCVAL(VPSPX0,HTK32)
MC1_S_3 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK3) ARCVAL(VPSPX0,HTK9) ARCVAL(VPSPX0,HTK15) ARCVAL(VPSPX0,HTK21) ARCVAL(VPSPX0,HTK27) ARCVAL(VPSPX0,HTK33) ARCVAL(VPSPX0,HTK3) ARCVAL(VPSPX0,HTK9) ARCVAL(VPSPX0,HTK15) ARCVAL(VPSPX0,HTK21) ARCVAL(VPSPX0,HTK27) ARCVAL(VPSPX0,HTK33)
MC1_S_4 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK4) ARCVAL(VPSPX0,HTK10) ARCVAL(VPSPX0,HTK16) ARCVAL(VPSPX0,HTK22) ARCVAL(VPSPX0,HTK28) ARCVAL(VPSPX0,PIBCLKB0) ARCVAL(VPSPX0,HTK4) ARCVAL(VPSPX0,HTK10) ARCVAL(VPSPX0,HTK16) ARCVAL(VPSPX0,HTK22) ARCVAL(VPSPX0,HTK28) ARCVAL(VPSPX0,PIBCLKB0)
MC1_S_5 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK5) ARCVAL(VPSPX0,HTK11) ARCVAL(VPSPX0,HTK17) ARCVAL(VPSPX0,HTK23) ARCVAL(VPSPX0,HTK29) ARCVAL(VPSPX0,PIBCLKB1) ARCVAL(VPSPX0,HTK5) ARCVAL(VPSPX0,HTK11) ARCVAL(VPSPX0,HTK17) ARCVAL(VPSPX0,HTK23) ARCVAL(VPSPX0,HTK29) ARCVAL(VPSPX0,PIBCLKB1)
MC1_Z_0 (A)*~(B+C+D+E+F+G+H+I+J+K+L+M) 13 WIRE(VPSPX0) ARCVAL(VPSPX0,HTK5) ARCVAL(VPSPX0,HTK4) ARCVAL(VPSPX0,HTK3) ARCVAL(VPSPX0,HTK2) ARCVAL(VPSPX0,HTK1) ARCVAL(VPSPX0,HTK0) ARCVAL(VPSPX0,HTK5) ARCVAL(VPSPX0,HTK4) ARCVAL(VPSPX0,HTK3) ARCVAL(VPSPX0,HTK2) ARCVAL(VPSPX0,HTK1) ARCVAL(VPSPX0,HTK0)
MC1_Z_1 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK11) ARCVAL(VPSPX0,HTK10) ARCVAL(VPSPX0,HTK9) ARCVAL(VPSPX0,HTK8) ARCVAL(VPSPX0,HTK7) ARCVAL(VPSPX0,HTK6) ARCVAL(VPSPX0,HTK11) ARCVAL(VPSPX0,HTK10) ARCVAL(VPSPX0,HTK9) ARCVAL(VPSPX0,HTK8) ARCVAL(VPSPX0,HTK7) ARCVAL(VPSPX0,HTK6)
MC1_Z_2 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK17) ARCVAL(VPSPX0,HTK16) ARCVAL(VPSPX0,HTK15) ARCVAL(VPSPX0,HTK14) ARCVAL(VPSPX0,HTK13) ARCVAL(VPSPX0,HTK12) ARCVAL(VPSPX0,HTK17) ARCVAL(VPSPX0,HTK16) ARCVAL(VPSPX0,HTK15) ARCVAL(VPSPX0,HTK14) ARCVAL(VPSPX0,HTK13) ARCVAL(VPSPX0,HTK12)
MC1_Z_3 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK23) ARCVAL(VPSPX0,HTK22) ARCVAL(VPSPX0,HTK21) ARCVAL(VPSPX0,HTK20) ARCVAL(VPSPX0,HTK19) ARCVAL(VPSPX0,HTK18) ARCVAL(VPSPX0,HTK23) ARCVAL(VPSPX0,HTK22) ARCVAL(VPSPX0,HTK21) ARCVAL(VPSPX0,HTK20) ARCVAL(VPSPX0,HTK19) ARCVAL(VPSPX0,HTK18)
MC1_Z_4 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,HTK29) ARCVAL(VPSPX0,HTK28) ARCVAL(VPSPX0,HTK27) ARCVAL(VPSPX0,HTK26) ARCVAL(VPSPX0,HTK25) ARCVAL(VPSPX0,HTK24) ARCVAL(VPSPX0,HTK29) ARCVAL(VPSPX0,HTK28) ARCVAL(VPSPX0,HTK27) ARCVAL(VPSPX0,HTK26) ARCVAL(VPSPX0,HTK25) ARCVAL(VPSPX0,HTK24)
MC1_Z_5 A+B+C+D+E+F+G+H+I+J+K+L 12 ARCVAL(VPSPX0,PIBCLKB1) ARCVAL(VPSPX0,PIBCLKB0) ARCVAL(VPSPX0,HTK33) ARCVAL(VPSPX0,HTK32) ARCVAL(VPSPX0,HTK31) ARCVAL(VPSPX0,HTK30) ARCVAL(VPSPX0,PIBCLKB1) ARCVAL(VPSPX0,PIBCLKB0) ARCVAL(VPSPX0,HTK33) ARCVAL(VPSPX0,HTK32) ARCVAL(VPSPX0,HTK31) ARCVAL(VPSPX0,HTK30)
The above shows the sets for the wire VPSPX0. Only one pair of ARCVAL signals can be active. A bit of a thing is that in each line the first six ARCVAL pairs are repeated in the next six. This might have to do with FPGA's with a bigger density having more global clock lines, but I'm not sure on that.
I now have to write some code to do a reverse lookup from the bits set to find which HTK or PIBCLKB signal is active.
Another thing I have to modify in the code I made is that the global clocks are not FPGA global, but half FPGA global. For instance GCLK_0 can be a different signal in either half. Despite the fact that the block diagram of the clock systems shows quadrants and there are four central clock multiplexers, the first set of 8 vertical lines is multiplexed by the lower central multiplexer and the next 8 vertical lines are multiplexed by the upper central multiplexer.
Lots of puzzles still to be solved.