Brief Answer:
Rest and medicines as advised

Detailed Answer:
Hi.
Thanks for your query.
Read and understood the history and your complaints.

To recapitulate:
Female / 53 - H/O Pulmonary Embolism - MRV done 2 weeks ago - getting over stomach flu- cramps on lower abdominal muscles and Low back ache - hurts to cough...

Since you had suffered from Pulmonary embolism and underwent Pelvic MRV recently, the overall resistance power of the body is already at stack, which is enhanced by flu.

This is the reason you are still getting crampy lower abdominal muscles and lower back pain.
The cause of pain on coughing indicates that both the muscle groups are still inflamed and need treatment:

I would suggest the following in such a situation:
Bed rest - rest is important part of the recovery process.
Plenty of oral fluids - well hydrated body recovers well.
The pain and the muscle spasms go hand-in-hand; meaning whenever either of the things ( pain / spasm) increase, the other automatically increases. Hence this vicious cycle has to be broken. This is possible by taking the medicines for spasm and pain in the form of muscle relaxants and Pain killers. These you have to take in consultation of your Doctor since you are recovering from the past problems and your Doctor would only tell the best options for you.
If you have been already given medicines for such a purpose, take them in full dosage and as per schedule.

Take cough suppressant.
Laxatives if constipation.
Multi-vitamins in the form of anti-oxidants, help in recovery.
Local rubrafascient (which increase local temperature and gives feeling of smoothness) ointments or liniments also help a lot.
Avoid cold places as this increases muscle spasms .

I hope this answer helps, I have tried to include even the minutest points for recovery. Please feel free to ask for more if you have further relevant questions or if you feel that there is a gap-of-communication.

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