Did they measure your prolactin in new tests?
The testosterone / estrogen ratio totally depends from many other hormone functions to your body stats ( overweight etc ). Everyone needs to test it to know for certainty and results are individual. Low T does not necessarily equal low E2.
Clomid will bind itself to estrogen receptors fooling your brain to think there's little estrogen present, this will increase LH/FSH which in return stimulate synthesis and secretion of testosterone.
Tests will propably show your estrogen levels are from good to high, i guess, and i don't have enough knowledge to say how human biology works in this matter regarding if such results with clomid in action should be treated as false?
Hopefully someone will fill us in.
Editing this post further:
I had little time to study more about the doctor / clomid relationship and long term use hehe.
There's no real studies about !long term! usage of clomid with males unless one has been done recently, i doubt that very much.
Check out this funny link as one example: http://www.ncbi.nlm.nih.gov/pubmed/22458540 "Clomiphene citrate is safe and effective for long-term management of hypogonadism" published in US national library of medicine concluded by 5 doctors study.
Pretty much only thing they concluded hypogonadism wise, is that clomid raises T levels considerably and because they tested it with males who were treated with clomid for over 12 months ( not specified exactly how long ) it's therefore a viable long term treatment for hypogonadism. Since none of the 46 patients in the experiment reported no sides, they concluded it safe.
It doesn't sound even remotely right though.
Clomid is serm, and in lords year 2015 they are still not fully understood even though they've been around for decades. There's a lot of interesting information about them.
Reported side effects with users ranging from blurred vision to nausea, mood crashes to loss of libido etc. Bioactive testosterone is very doubtful aswell with long term usage due to estrogen agonist properties.
I could go on a lot about this but everything to me says this treatment is not going to be long term and should only be short term plan at best. Think about it, it makes no sense.
If your doctor thinks estrogen blocking with serm is the way to treat your hypogonadism for the rest of your life, he is an idiot and treats you as a guinea pig. Imo you should take the traditional way but that's just my opinion.
All the best bro, and be sure to post the results in september.