Won't hurt to get the thrombophilia and ANA/APA tests done just to rule those out (especially as insurance will cover that). Then try also getting an endometrial scratching done and give it three months naturally or do it along with your next IVF cycle.

Bacterial infections can also cause implantation problems. Very often they're symptomless.

FYI, here's a good write-up on problems with the endometrium that can prevent implantation:

http://medicine.yale.edu/obgyn/kliman/Images/For%20Patients%20(About%20EFT)_tcm607-152161.pdf

I'm pretty sure the tests you mention above are all for clotting disorders. Research suggests that some of these could impact implantation, but the bigger issue with clotting problems is usually recurrent miscarriage. The other big potential issue with implantation is immunologic rejection, which is extremely complicated but here's a good explanation:

http://haveababy.com/fertility-information/ivf-authority/understanding-immunologic-implantation

Ive had two IVF cycles so far. One ended in ectopic and the other (which was FET) did not implant, despite having a wonderful blast. I am considering doing another cycle and my RE is very positive about it. BUT he was also very encouraging about the previous two failed cycles. My REs did not offer any reason for the failure of the 2nd and I am concerned I may have an implantation issue. My friend who is a nurse at another fertility clinic sent me some info on tests they do at their clinic. The tests are Factor V mutation, factor 2 DNA analysis, Protein S, ProteinC, and Lupus anticoagulant.

Has anyone had these tests or other "implantation" testing?