Hello,
It looks You don't have NET in this VR and hence no ISIS adjacency.
Please add these lines:
set interfaces lo0.100 family iso address <NET>
set interfaces lo0.100 family inet set routing-instances Custom-VR interfaces lo0.100 set routing-instances Custom-VR protocols isis interface lo0.100
As to why You cannot ping to directly-connected IP - please make sure You issue ping command with "routing-instance" option.
HTH
Thx
Alex