Best advice I have is to print the 20mmx20mm makerbot test cube and watch it print every layer while observing how it is acting. There is endless amounts of free information regarding how a printer should print and what it should look like. Simplify3d has a free cause and effect pdf. file that is very helpful in determining problems and causes. If you use the makerware software be careful because the default settings will not work well on the printer. Using makerware is better than the replicator software when you get it setup right. Here is a link to my Thingiverse designs where you will find .json files for the QIDI (Thingiverse - Digital Designs for Physical Objects 30). One for PLA and one for ABS. Download the latest version of makerware desktop and follow videos on youtube of how to import .json files into profiles. The files I created work well on my QIDI and should provide any QIDI user with a point to start where your prints are good and just need a little tweaking. When setting up makerware desktop remember to use makerbot dual printer profile only. After having my printer for a year I have managed to achieve prints as good quality as prints from a u-print or dimension printer.
If aligning the nozzles is the issue, then there is another more reliable way than using shims. Using which ever nozzle you determine is lower, just print out this object from einer_design:
Remove your heat block, and screw this fixture into the bottom of it. Then loosen the set screws for each extruder and push them down firmly and re-tighten the set screws. Guaranteed a set of perfectly aligned nozzles. 
Another GREAT upgrade to this machine is to consider installing the Sailfish firmware on it. Makes the machine run smoother, faster, and produces better quality prints.
I’m puzzled by this.
My QIDI came with sailfish!?
It already has Sailfish. DO NOT update without talking to QIDI first. If I remember correctly, the Sailfish version is modified and people who updated bricked their printers.
These blocks are great but sometimes it is the carriage that is slightly off as is the case with mine.
My QIDI is over a year old now, and did not come with Sailfish. I guess they realized the benefit to running Sailfish and have started rolling out their printers with it already installed. That’s great to hear. You can ignore my previous comments about it. 
I didn’t realize they didn’t have some time back. I remembered some trying to update it this past spring and running into issues bricking the board. Maybe it wasn’t until early this year they switched then. Good to know and watch for on older ones.
The einer_design thing looks great. Are the set screws accessible on the QIDI by just removing the two screws on the bottom to pull the extruder head off then screw this on the bottom, or is there a little more surgery involved? I had read something about set screws being on the back side but didn’t look. It would be great if one could just remove the head, put this on, loosen the set screws, level the nozzles, tighten the set screws, put the head back on. Done.
Yes, they are on the back.
So turns out that a wire for my motor had broken after checking it with a continuity tester. After replacing the wire my printer works great except for the left extruder. I can easily load filament and it puts out the first line on the platform fine but then stops feeding. The filament is correctly loaded but for some reason it hear a clicking sound and the filament is not fed through. Could it maybe be a jam? I dont think it would be because it works for the first line as I said but then stops.
Sounds like the spacing from bed to nozzle is to small. Re-level and see how it goes. The clicking is the extruder stepper trying to go but can push the filament.
I’m literally having the exact same problem. I tried. contacting support and they were not helpful at all. Have you figured out a fix?
Im also having a problem with installing the MK all Swiss nozzle, the hot end will not come out of the silver block. Does anyone have a fix for that? It’s supposed to slide out easily (and yess I did take out the screw at the back of the sliver block, it’s a tiny black screw)
please help!
I personally have not tried a Mk Swiss nozzle as I just use the stock one. As of yet I have not found a fix for the second extruder which is frustrating because I got this printer for the dual extrusion capability. With your nozzle issues the Swiss nozzle might not have the same threads as the printer does. I have noticed after checking the wire holder bolts that they use an odd form of measurement so that may be the issue.
The unit of measurement is SAE / imperial. SAE stands for society of automotive engineers. Thats the unit of measurement on the wire bolts so it may be the same for the nozzle threads.
I have leveled the bed perfectly and I hear the clicking but it won’t extrude when it starts printing but I can load the filament easily.
Turns out the one of the stepper motor wires broke. After replacing it I was able to get perfect prints. A quick question though. My rafts are sticking a bit too well to the prints. I can get them off but with a lot leftover thus requiring me to use a razor to pick it off, any tips?
Again, that sounds like the nozzle is to close to the bed. The clicking is the extruder skipping which basically means something is restricting the filament from being able to extrude. So, if it extrudes ok when loading but stops when trying to print there are only a few things it can be.
Nozzle to close to the bed.
Temp not high enough for the filament and the speed.
Some other obstruction or binding.
Level the bed and then lower it away from the nozzle a bit so there is a bit of space and then see what happens.
Also what are the settings for the first layer plus temps etc.?
Another thing is make sure there is nothing binding the filament as the gantry moves. Possible for it to get pinched.
This is not uncommon. The barrel gets a “notch” in it from the screw and that hangs on the bore. I have one that is so stuck I will have to drive it out with a punch.