Finsky, are you saying that I should remove the second box?
You wrote: I have a small package colony that I installed May 8th.
If you had 1/2 langstroth box of bees, it is impossible that hive had raised bigger than it was when you get bees. First bees emerge 21 days after egg layins. Let's say that queen stated egg laying 5 days after installing. So those brood are 31-13= 18 days.
If queen started at once 31-8= 23. The first are just emerging.
And you have so cold weather that you cannot open the hive.
Also, I do see lots of capped brood and quite a bit of honey, the frames look great that they are using, but shouldn't I be seeing alot of uncapped larvae at this point? I am not seeing any and am now worried that my queen may have died
If it is dead, you should see emergence queen cells in frames.
If you had not, queen has stopped her egg laying.
OR, they have renewed the queen at once and you have now a virgin queen inside hive which have killed the queen. But time table does not math to that.
Queen development 14 days and after that worker larvae are to be seen 10 days. = 24 days? Don't match or it is very near.
now it looks like we will have several weeks of rain and high in the 60's. Will I chill them if I open it when the colony is so small? I appreciate your advice. Thanks!
60 is too low. But if weather is sunny and no wind blow, you may quickly open the hive. We have here now almost all the time 60C but sun is often shining. Small hive suffers from opening more than big hive.
Normally it is not wise to open hive under 63F and then it should have bright sun too.
I open even if snow is on ground but it is not wise.
If you have had bad weather and bees not get pollen, worker have perhaps destroyed larvae. It happens. When you open, llook ido they have pollen in combs. If not, they are starving.
And look, if bees do not cover all frames in lower box, you have too few bees and that upper box is harmfull for progress. If you keep it, put it under brood box.