See if you remove the power to the stick for a minute, then reconnect the power and go through the pairing process again following these instructions.
Last resort, try a factory reset.
With the stick and TV switched on, hold in the small reset button on the stick for about 15 to 20 seconds.
Please note if you factory reset the stick you will have to setup the stick again from scratch and make sure you use your existing now tv account details when requested.
The stick does run pretty warm, if you have a HDMI port on the side of the TV then maybe try that to see if it improves the ventilation and wifi signal around the stick.
Also maybe try the supplied power adapter plug has well with the stick if you are currently using the USB port on your television for power to the stick.
Try new fresh batteries.
I am also assuming the replacement remote is the same version has the original remote that has the voice search option and the volume buttons on the side ?
If nothing works, have you got another television at home to try the stick on ?
You could also maybe try a quick power down and reboot on your Router before trying the stick again with your new replacement remote.