I didn't make an exact record of this but I've been having a different kind of intense throat pain when I wake up in the morning  (not anything like it was from a cold) since starting T. Is this a side effect of the hormone? If so, am I going to suffer with this every day from this? By the way, I am taking a low dose gel.

I did have a sore throat that felt different from a cold when I experienced the first two vocal cracking periods, but it wasn't extremely uncomfortable. It just felt like I had been talking/singing too long without drinking anything. It did go away in my case, but keep in mind that there are strains of the flu floating about and when I had it in Jan that was the worst sore throat I had ever experienced.

Since I'm on injections I can't really say if it's a side effect or not. You might want to read the prescription pamphlet and see if it could be a gel related side effect. As far as I know it's not listed as a side effect of the injectable (intramuscular) testostrone cypionate.

If it becomes bothersome, gets worse or stays around for more than a week I'd consult with my doctor if I were in your shoes.

"Intense" throat pain?  That's definitely not normal and should be checkout out by a doctor.  What other symptoms are you experiencing?  Swollen lymph nodes?  Fever?  Bad taste in your mouth? 

Yes, the other day the pain lasted the entire day. Now, I wake up with the pain but it goes away after an hour or so. I don't think I have other symptoms you mentioned so I am guessing it could be due to voice changing?

Well, I've never heard of anyone's voice changing causing "intense" pain, that's abnormal IMHO.  I would ask your doctor about it, mate. 

How would you describe "intense" makipu? Pain is all relative to the person experiencing it after all. Intense pain for me for example is very extreme pain for many people and a mere tickle for one of my friends. Is it a scratchy pain? A burning pain? Throbbing? Constricting?

But in any case I do agree with Kreuzfidel that if you are questioning why your throat hurts its time to consult your doctor. Thyroid problems are a key reason to do this, since they are located in that area and are affected by hormones. Better to check a potential health risk off the list than to wonder. Plus a doctor can give you way better advice than a bunch of people online, especially when it comes to your health.