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I'm not entirely sure on (1) without seeing how you have stopped the display at 90. One thing of note: if you are bringing in a button (or switch), be sure to sync it to your clock before using the signal to control anything. All it takes is one or two registers to properly sync it to the clock.
For (2), verify that your timequest timing analyzer report indicates you have no timing errors and no unconstrained paths. If you do have problems - fix these first. Also, it would be a good idea to add a register stage for your switches too. I won't go into detail unless you are interested.
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I probably stopped the clock the dumbest way possible but I'm a complete newbie when it comes to Quartus and most of the time the answers you guys give just fly right over my head.
To stop the clock I made the input for the 10's place (2nd digit) a 3 input and gate. The first input is the clock itself, the second input is the switch that turns the clock on and the 3rd input is where I took the output of the 2nd digit used the lpm_compare tool and said when the output equaled 9 to output a 0 which I inverted and tied back in to the beginning of the 3 input and.
As for (2) this is all I can really add, the adder works just great when its in its own project, but when I add a clock it stops working...even if I delete the clock back out and remove it from the project that adder still doesnt work then.
What's a register stage?