So I have got my Smartrap to print but when I hit about 30-50 minutes into every print it starts to get flow failures. The gear is not skipping not slipping and the motor is ice cold and is working fine. What could the issue be?
I also want to order one of @Brook_Drumm 's all metal ubis hotends but my fear is that it will melt the top plastic hole. Would it work or do I have to try another type of hotend?
The all metal ubis hot ends are 100% room temperature up at the mounting point. They aren’t going to melt anything that you don’t want to specifically melt by putting it through in filament form. 
Well I had the current to where the motor was hot and I’ve progressively turned it down until now it is id say slightly warm. But I do get some very fine power on my mk7 gear
I’d check on your printer’s forums and ask what voltage/current setting is optimal for your extruder and tune it that way - steppers will run hot normally without active cooling anyway so I’d agree that you are likely under powering it at the moment. Get the old multimeter out and set it properly and I suspect your issues will disappear.
I’ve tested it at heats where the motor is burning hot all the way down to ice cold. I don’t think it is the motor. And I know the hotend is set up correctly because it is a preconfigured hotend and @Javier_Prieto has the same and we share the same settings and he is 100% successful with his.
Motor temps are simply a mechanical response to friction and can vary hugely depending on load, speed etc. My point (and Marks above) is that if the Motor is cool when running, it’s probably not got enough current to handle the filament feeding if the torque increases for example because the spool gets stuck, or some plastic cools a little in the hot end and increases the work it needs to do. For example on my old Huxley, I had exactly this issue, and properly setting the current to 0.45A on the driver fixed it completely. Depending on your electronics, your power requirements may be different. I also worried about stepper heat on long jobs, and added an active fan for the extruder motor, but honestly other than making me feel better I don’t think it changed the steppers performance. Under powering the steppers will also cause other print quality issues which can be difficult to figure out later.
The problem is most likely heat rising and causing a jam.If the motor is cool and is feeding before that, it is not going to suddenly cause a problem much later in the print.
So should I run a fan on the hotend itself? I have a little one lying around I can make a bracket for
If You are using the Jhead lite hotend as I can see on your photo, then you must use a fan always turned on to cool the peek piece of hotend. The best and easy way is to just connect some fan to the power supply. I was using this little hotend with fan mounted like this and it was just fine 
The second fan can be connected to the ramps and used to cool the print, but the fan for the hotend is necessary. Otherways your hotend and mounting arm will just melt (yup, I have survived that somehow)
And you were saying that your motor is getting hot. Then you are having too much current on the stepper driver for sure. When you will start using fan on hotend, the filament will need less power to be pushed throo the nozzle, so lowering the current should help then. I was suffering for this also, because of the bowden extruder. You can try to replace it with the geared one. I was using the RegPye’s geared extruder (from reprap forum) and it was working like a charm.
Ok cool!! Thank you @Kamil_D !! This may sounds stupid but what part is the peek? Is that yeh white part or what other part?
@Kamil_D that hotend does not need fan cooling. I have heated it to 230 degrees and you can grab it by the top part because is only warm
Also my long time printings (5h and a half) did not required that fan, and Ohioplastic says that it is not neccesary. I only have had a jam in three months printing 10 hours per day, and it was because dust
@Javier_Prieto Oh, then you are lucky one. Mine just needed this, or the arm was melting. And besides this, everything is just like you have said, it’s really good hotend
Try seeing if your thermistor is seated properly in your hotend if it is loose it might be giving the wrong reading causing it to report the wrong temperature to the software.
The fan has solved the problem. And then died after about 5 hours. Pays to buy expensive stuff? I think not in this case. I’ll stick to my cheap $2 fans from now on.