http://img96.imageshack.us/i/spectro1.jpg/
For question 2, I think I have to change the Rhydberg constant (by altering μH the reduced mass). After that I'm not sure how to handle the question?

For question 3, can I just use the Energy formula C [inertial constant]*(pi^2/mL)*n^2 ?? If so, would n be (4^2 - 2^2) ?

Hi
You are right
here in both the cases only reduced mass of element is changed
so you will get RA value different from RH value
The value is different for both 4He+ and 3He+
yes
you are right again you have to use formula for energy in one dimensional box
n(final) = 4
n(initial)= 2

For question 2, Should I be using mass in kg or u ? What does it mean by the two lowest energy "Pfund-series" type lines?
mass is taken in Kg because in Rydberg constant we have taken mass of electron in SI units(Kg)
Pfund series are formed when electronic transitions are taking place from n=5 to any value of of n>5
hence two lowest transitions are :n=5 to n=6 and n=5 to n=7

Okay, mass is in u. I calculated the reduced mass of 4He+ and the reduced mass of H. Then I divided the Rhydberg constant by uH and multiplied it by u4He+ to get a new constant.  Is that correct? If so what do I do next?

Can I use the equation ~En=-R4He+*(Z/n^2) ? Where ~En is the energy in cm^-1, R4He+ is the new Rhydberg constant, and Z is the nuclear charge. What would the values of n be?
yes
you are right here energy is in the form of wavenumber
now to take out energy of transitions from n2=5 to n1=6
v(wavenumber) = R(1/n1^2- n2^2)
where R is the new Rydberg constant which you calculated for 4 He+
second lowest energy is given by
from n2=5 to n1=7
v(wavenumber) = R(1/n1^2- n2^2)

for the second  b part
you just need to change Rydberg constant for new isotope of He --3He +