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You should assign the pin according your CPLD's pin connection on the PCB, the software assigns these "INPUT/GLCRn) and the second pin(INPUT/OE2) were 'GND' " is that these pin is not used in your design, it is best to tie them to GND.
The AHDL is like ABEL language, it can get better and more explicit control over the generated logic, but it is too waste time and the simulating is a problem if your design is not simple
Because 74HC series IC is not high impedenc when power is off, so your circuit will not work, change the 74HC541
to TI's correspond 74 series IC, such as 74LVCT541, 74LVT541, 74AHCT541 and 74ABT541.They are support hot swap(when it's power is off, it output pin and input pin are high impedenc)
The new device Stratix G series have front high speed SERDES. The Stratix's
differential pairs surport more standard but its pin is not flexible than Virtix-II, its
differential pairs are fixed as input or outputcan, and Virtex-II's differential pairs can be programmed as input or output.
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