Planning to breed....

Question
We have a female AKC registered boxer who is going to be 4 in August.  We got her as a gift from my husband's uncle who owns the dad (I know that is not the technical term).  My husband's family has had boxers for almost 25 years and they carefully breed them on occasion to keep the family line going, and we were told that our dog was a gift as long as we choose to breed her to keep the line going as there are not many left who haven't been spayed/neutered.  We said that was fine and planned to breed her once and make sure that at least 2 of her puppies stayed in the family, then get her fixed and be done.  My husband remembers his family breeding his dog when he was a kid, but that was 20 years ago and he doesn't remember most of it.  
Is 4 too young, is there an age that will be easier/safer for our dog?
The bigger issue is that she goes into heat with such irregularity we never know when it will happen.  She is currently in heat, but the last time was last June.  Will this be a problem?
Does the size of our dog matter?  She is small for a boxer, weighing in at about 40 pounds and is shorter than all of the other boxers in the family.  Her mom dog was pretty small, but had broader hips than our dog.  My husband's uncle thinks she is too small, but the vet has never said anything and he knows we intend to breed her.
I just don't want anything to happen to my girl.  Her "grandma" died after having a litter due to an infection that no one caught.
Any information would be helpful, thanks!

Answer
I'm so sorry this took so very long to answer. I had internet problems.

Question 1) Is 4 too young, is there an age that will be easier/safer for our dog?
Answer: My personal opinion on this age matter is 4-5 is cut-off on breeding. Age 2 years is best as they are young, but they are emotionally mature enough to be maternal and physically well. Age 4 is pushing it. A Boxer's average life span is 10 years old, and she is almost half finished with her life. Also, at ages 4-5, they begin to have health issues: hip dysplasia, many different cancers such as mass cell tumors, lymphoma, heart problems, and thyroid disorders which is very common in Boxers, etc. And, you mentioned her heat cycles are irregular: heat cycles are every 5-6 months and last approx. 28-30 days.
http://en.wikipedia.org/wiki/Hip_dysplasia_(canine)
http://www.vcchope.com/resource-center/cancer-in-dogs
http://www.vetmed.wsu.edu/deptsOncology/owners/mastcell.aspx
http://www.wearethecure.org/lymphoma
http://www.ncbi.nlm.nih.gov/pubmed/19379305
http://americanboxerclub.org/purina6.html
http://americanboxerclub.org/genetic_diseases.html
http://americanboxerclub.org/purina3.html
http://www.gentryboxers.com/thyroid-problems.html
http://pets.webmd.com/dogs/hypothyroidism-in-dogs
http://en.wikipedia.org/wiki/Boxer_cardiomyopathy
http://www.petmd.com/dog/conditions/cardiovascular/c_dg_cardiomyopathy_boxer
http://www.examiner.com/article/boxers-101-health-issues-boxers


Question 2) She is currently in heat, but the last time was last June.  Will this be a problem?
Answer: Yes, this is a problem. Heat cycles are every 5-6 months and last approx. 28-30 days. If her heat cycle was that extreme; 11 months ago (between cycle) then she has a health problem and should not be bred. Irregular menstrual cycles (even in humans) are generally a sign of a thyroid disorder. If she was to get pregnant, then two things will occur: 1) she can abort the puppies due to the thyroid disorder, and 2) if not abort and delivers, her puppies will 90% inherit her thyroid disorder as generally, puppies are more apt to inherit from the mother. I recommend getting her thyroid checked ASAP!

http://www.pet-happy.com/abnormal-heat-cycles-in-female-dogs/
http://www.yourpetsbestfriend.com/your_pets_best_friend/2007/02/dog_heat_cycle_/

A quote on a message board: "Irregular cycles can be caused by thyroid problems as well. Ive had more than one dog with estrus problems that turned they could not conceive and tested positive hypothyroid. I actually have a male now with NO sex drive and he too is dx as hypothyroid. Its worth checking out. IMO hypothyroid is genetic and dogs that pass it on should not be bred. There is nothing more frustrating than buying a bitch only to find out that not only cant she conceive, she is hypothyroid and needs to be on meds for the rest of her life."

Hypothyroid:

http://www.allboxerinfo.com/Hypothyroidism.html
http://www.vetmed.wsu.edu/cliented/hypothyroidism.aspx

Hyperthyroid:

http://www.petmd.com/dog/conditions/endocrine/c_dg_hyperthyroidism
http://dogcare.dailypuppy.com/causes-canine-hyperthyroidism-4782.html
http://www.newcastleboxers.com/thyroid.shtml
http://www.nativeremedies.com/petalive/articles/out-high-cortisol-levels-hyperth
http://animalendocrine.blogspot.com/2012/06/thyroid-tumors-and-hyperthyroidism-i
http://www.nativeremedies.com/petalive/articles/out-high-cortisol-levels-hyperth
http://www.vetinfo.com/causes-of-thyroid-problems-in-dogs.html#b
http://www.boxerworld.com/forums/dog-health-issues-questions/156353-possible-hyp

Question 3) Does the size of our dog matter?  She is small for a boxer, weighing in at about 40 pounds and is shorter than all of the other boxers in the family.  Her mom dog was pretty small, but had broader hips than our dog.  My husband's uncle thinks she is too small, but the vet has never said anything and he knows we intend to breed her. I just don't want anything to happen to my girl.  Her "grandma" died after having a litter due to an infection that no one caught.
Answer: Yes, the size matters. A small female shouldn't breed with a larger male because puppies could be larger and cause a difficult whelping. Also, I am extremely concerned that a 4 year old female Boxer only weighs 40 pounds. That is under weight and can be another symptom of a thyroid disorder or even diabetes. If her grandma dies after whelping due to Eclampsia or Metritis............

http://www.medicanimal.com/viewarticle/~contentId=111510/~nodeTrailCsv=AR-DOGS-P


My recommendation:

Get a new vet. The one you are using is not Boxer-savvy and is ignoring the obvious of her underweight and your intend to breed because he/she is not giving a health check: blood test for thryoid disorders, x-rays of hips, etc.

DO NOT BREED HER.