I’m with many of my collegues. By 8 weeks you should be starting to see some reduction in pain. Although the pain may not completely be erased. If you are not, I would follow up with your physical therapist or physician.
It is also important that you are monitored in the way that you are performing the exercises and that you complete any homework your physical therapist may have given you. If you are unsure of how to perform different exercises or how often you should be given the various homework your therapist has given you, then please ask them to clarify. If your therapist did not give you any work to do at home, I would ask them what you should be doing between your sessions to help ease your pain and then to strengthen your weak areas and strengthen your overly tight ones. Usually where there is pain there is an imbalance and over-compensation, so it is important to strengthen and stretch the cooresponding areas.
And as Karin said, if you are not already seeing a physical therapist and/or physician for your pain, please do so. A personal trainer is often ill equiped to diagnose your problem and if there is pain, you should always be seen by a physician to receive treatment, not a personal trainer.
I hope that PT stands for physical therapist and not personal trainer as it is beyond our scope to diagnose problems and prescribe exercises for it.
If you have done the exercises correctly and as often as recommended, then there should be some improvement at this point in time. If this is not the case, I would refer back to the physical therapist. Others have suggested alternatives as well but I would start with the PT and take it from there.
I hope that you will be out of pain soon.
There are a few considerations that you may want to consider as a holistic way to treat your pain.
First off, it sounds as if your physical therapist has covered some exercises for you, which will help to build strength if indeed, your arm are weak and a muscle imbalance is causing your pain. The way you perform the exercises is important, so an experienced trainer may be able to help you troubleshoot your form & adjust your other workout components appropriately
Muscle imbalances often stem from improper ergonomics at your workstation, at home, etc. It would be useful to get an ergonomic evaluation from an expert – many products that are marketed as ergonomic are not truly good fits for people.
For immediate relief, you could seek out various forms of manual therapy. Your PT would likely have a TENS unit, and could recommend a home version if it appeared to help with your pain. Someone else mentioned massage, but you may benefit from finding a person with specific experience in trigger point release, fascial stretch therapy, or strain/counterstrain therapy. The qualified practitioners for these types of treatments range from massage therapists, personal trainers, PTs, and occupational therapists, so depending on your area, you may have to search around a bit.
Are you currently practicing any stretch techniques? Sometimes, trying to power through a problem without proper rest can cause overly sore muscles, and therefore, more pain. You may want to explore some yoga/relaxation breathing practices to help aid your recovery.