The 390 will be quicker and more nimble but they can be plagued with electrical issues (TC and ABS), previous models suffered from overheating but that might have been addressed with newer models. The KTM's engines are worked a lot harder, take that info as you will.
Check the major service pricing on the 310, seems high but I'm not 100% clued up on the smaller cc service pricing.
Re KTM parts taking 2-3 weeks, anything I bought that was not a standard replacement (filters, chains..) took long.
My new 690 ECU blew randomly, 10 Weeks, tail light stopped working, 8 weeks, the front ABS sensor, 5 weeks. All were covered by KTM warranty
Ride the ones that feel's good.
Edit: I do agree the Ninja 400 is a fantastic bike and probably the quickest of them all but check maintenance times and costs. Its also very much limited to road where the 390/310 have the ability to ride gravel and take luggage.