I'm not sure what voltage the red LED inside the NES is rated at. I'd
assume +5v because that's pretty standard for circuits with ICs. The
blue LED I put in is rated at +6v. So, running +5v into it should be
fine. There could be amperage issues. I guess it's possible that the
new LED could be trying to pull too much juice, but I doubt it.

I've had my NES since around 1990, and it's got tons of hours on it.
So, dirty contacts and general wear and tear are probably issues,
too. In any case, I disabled the lockout chip on the NES and now
everything works fine. Actually, I'd say everything works great.
Disabling the chips is probably the single greatest thing you can do
to a Nintendo.