I have been losing at least half of my shots. The grounds get dumped and the red exclamation point comes on. I have to fiddle with bean hopper or dredge drawer, then sometimes it will pull a shot.

the add beans to hopper signal most likely is triggered by the machine not sensing enough load put on the grinder (hence it thinks its out of beans) , this most likely is set by the grind (fine/course ) id say the grind is set to an improper size and the automatic sensor is picking up on that
another thing is the coffee / if its way too moist and not dry enough then its also going to trip the sensor as well

When the red exclamation point is flashing slow, something is not where it is supposed to be, bean hopper lid, door, brew mech, water tank empty, dregs box or water tray on dregs container is full. If the red exclamation point is flashing quickly, open the steam valve for pump priming. If pump turns on, and water passes correctly, the light should go off and return to heating stage. If not, we have a blockage or a pump that is not working correctly.

is the water available for brewing? are there enough beans for brewing? is there anything that shipped with the unit blocking the grounds?

Are you talking about the coffee brewing system? Or the coffee grinding system? You said "gears" so it sounds like you took the coffee bean hopper out and the adjustment knobs come out with it. So if you are trying to line those gear teeth back up correctly, Here is the complete instructions for cleaning the grinder (from wholelattelove.com). You only need the last few steps for lining up the gears.

You do not need to clean the grinder as often as you may think. Usually we do not recommend cleaning the grinder unless there is a problem with calibration or a clog. Avoiding oily beans, flavored beans, and beans stored in the fridge or freezer will typically prevent issues.

If you do experience issues with your grinder, cleaning it is the most common solution. To clean your grinder, follow these directions:

1. Remove the water reservoir, turn off and unplug the machine.
2. Take the cover off of the bean hopper and vacuum out the beans.
3. Remove the 3 Phillips head screws that are in the bean hopper.
4. Lift up the bean hopper and set it aside.
5. Open the machine's service door and remove the drip tray and the brew group.
6. Remove the rubber gasket from the top of the grinder area.
7. The grinder is made up of 2 pieces. The inner piece has 4 tabs that the rubber gasket sits on. The outer piece has teeth in a ring on the exterior covering ½ the circumference.
8. Rotate the outer ring 180 degrees counterclockwise. You should be able to lift off the inner ring. There is a red spot on the outer collar which should now be facing the 9 0'clock position when you are at the front of the machine.
9. Vacuum out all of the beans and ground coffee.
10. If possible, use a small pipe cleaner to get grounds out of the "pathway" going to the front of the machine. It is located on the floor of the grinder at about the 5 0'clock position.
11. Above where the brew group would be located, there is a gray triangular tab attached to a door on a hinge. Pull down on the triangle - coffee grounds may come out.
12. Look above the trap door and you will see the other end of the chute. Vacuum out the chute and clean with a pipe cleaner.

Reinstalling

1. Drop the inner burr onto the grinder with the tab that has the red and blue marks facing the right hand side of the machine at approximately the three-o'clock position.
2. Rotate the outer collar so that the red mark lines up the red/blue marks on the inner burr.
3. Reinstall the rubber gasket that goes over the grinder. The slots in the gasket line up with the four tabs of the outer burr.
4. There is a straight piece located directly to the right of the grinder. This is your dosage control. There is a piece that can slide backwards and forwards on this dosage arm. Push this arm all the way to the back of the machine.
5. Set the knobs in the bean hopper to #0 on the grind setting knob. Set the doser knob all the way to the plus setting. Now place the hopper back into the machine.
Note: You may have to rotate one or both of the knobs, a small amount, to get the bean hopper to set down on its supports.
6. Install the 3 screws.
7. Replace the water reservoir.
8. Fill the bean hopper with a cup of beans.
9. Plug in and turn on the machine.
10. Reinstall the brew group and the drip tray.
11. Once the machine warms up, press the small coffee button. When the grinder comes on set the grind setting to 6.
Note: You may have to press the small coffee button twice or 3 times before the machine will make a cup of espresso.

Hi
With the bean hopper on, turn the grinder upside down. Rotate the bean hopper to loosen any grounds that might be holding the burr holder. Now remove the bean hopper and try again to remove the holder. Only the outer burr comes off, this way.

The beans are hanging up in the hopper and not falling down into the grinder...... wiggle it, give the beans a push, or go to a bean that is not so sticky....

You will have to remove the bean hopper,realign the grinder,then refit the bean hopper

HI
Its normal to relieve some water (half to 1 oz.) and coffee, but excess is caused by having the small knob in the bean hopper set to the minus side. Twist the knob towards the plus side but not all the way, as this can cause an over charge and dump dry grounds in the dredge drawer and not make coffee at all. Another cause is your grounds are too coarse. If this is the case, when the grinder is running twist the big knob in the bean hopper to a smaller # but only do 2 #'s at a time and then make at least 4 coffees before making the next change. You can get the grinds too fine and have an other problem.

Try this remove the brew unit and clean the screen, the red light is saying that it cannot push water through.

Hi
You have 2 knobs in the bean hopper. The small one is set to the most positive. Turn it back 1 click from the plus and that should take care of your problem. When you have a clean brew unit it will make the first coffee but a little coffee is left in the brew unit and when it tries to make the second coffee a full charge and the little that was left cause an over charge, and dumps the coffee without making anything.