The jumper creates its own pads so you no longer need the connectors. As a final test to make sure all is ok, export the gerber (which is what the fab will use to make the boards) and use a gerber viewer (I use gerbv from the geda project, but there are others and online versions) to look at the gerber output independent of fritzing. What you see on the gerber is what the board will look like, and in rare cases fritzing sometimes makes mistakes (although probably not in this case).
The problem with running the sensors on 5V is that their output that then goes in to the micro is at 5V and the micro inputs are not 5V tolerant (i.e. they are likely to eventually fail if you expose them to more than 3.3.V). As well as noted, the 5V pin running temp is only present if the USB cable is present and powered (which may or may not be a problem in your application, although unless you want the temp to not run if USB is unplugged it would be better to power it from a stable power supply). Note this warning from the adafruit mkr1000 page (I tend to like the adafruit pages for things because they have good advise and data sheets 
:
"Warning: Unlike most Arduino & Genuino boards, the MKR1000 runs at 3.3V. The maximum voltage that the I/O pins can tolerate is 3.3V. Applying voltages higher than 3.3V to any I/O pin could damage the board. While output to 5V digital devices is possible, bidirectional communication with 5V devices needs proper level shifting."
In your case the 5V sensors are driving 3.3V inputs and would need level shifting to be safe (in the temp sensor case which looks to be analog in, it is difficult to level shift it, not impossible, just not worth the trouble usually). Sure post the final layout, more eyes are always a good thing before commiting to buy boards .
Peter