My four peneth...
I go along with the ide of drilling and gluing the following day and moving the blanks in doors as well that has caused you problems..
As for taking off the 1mm (ish) off the cap end should not cause any major issues, however if it was the refill tube then I would agree with Walter and Neil and rip it off and Start again ..
As for gluing tubes in place.... Glue with what you are happy glueing with, I have used all types and methods, if it works for you then it works, stick to it (pun
)