I've had a few laparoscopies to remove cysts, and they found endometriosis as well. (level 3, I believe.) This wasn't done as part of fertility investigation but when I was younger (not interested in having kids) and simply had pain from the cysts and endo.
Now I still believe I have endo again, because of the massive pain I get, but not one of the fertility doctors (4 clinics) that I've seen have ever made any mention of it being a problem although I tell them I have had endo. I was barely 28 when I saw the first specialist, and we had male factor. We were told to begin with IVF and ICSI and the only investigation they did on me was regular bloodwork and ultrasound.
Now I'm at another clinic, and they did a hysterogram (or whatever that thing is with the dye) and ultrasounds but never suggested anything about the endometriosis causing trouble. I'm going to one of the major/top NYC clinics currently, and I figure they know what they are doing... yet I have read many blogs of women who have been told to do surgery and that their endo is a problem.
With that first IVF at age 28 we had only a handful of eggs retrieved. Four fertilised, two were transferred at day 3, and only one was frozen at day 3. I had a + beta and home tests, but it ended up being a chemical.
While I'm concerned that I may still have endo and that it is hurting our chances the doctors are not. Between the endo and immune issues (Lupus) I wonder if more should be done, but the doctors continue to treat those as non-issues. So...
Here is my take: Frankly, the surgery hurts plenty and I'd be wary of doing it when you have concerns about it. If you may be moving on to IVF I'd be pushing to begin it sooner rather than later. Too many women end up finding that their egg quality is poorer than anticipated when they did get to IVF rounds. Endo may not even be your real problem. (I'm so sorry if that sounds hurtfully negative. I really hope you get through this with a baby as quickly as possible. I've read many infertility blogs though and so these scenarios regarding egg quality are on my mind.)
I did have bad pain, and ibuprofen helped somewhat but not enough. I also had random pain and issues with my digestive tract from the endo. Some people have no pain at all and yet discover they have it.
If you are concerned about the surgery I'd press the doctor to find out how necessary it is. Is your doctor a fertility specialist? (It doesn't sound like it.) If not you better go to one instead, because there is no comparison. The clinics really know what they are doing, and beyond Clomid a regular gyno just isn't the right track for this.