Recon, I am just a nurse, but I will try to answer your questions as best I can, and if I don't know, I will flat out tell you I don't know, lol. Okay, hope this helps and answers some of your questions.
1) Assessments for lower back pain and hip pain might include things like, a question and answer period. When did the pain start, where did it start. What were you doing when the pain started. Rate your pain level at rest and in motion. 90 percent of forming a correct diagnosis is in the history portion of the exam. And due to the nature of your wife's issues, he will also discuss all medications she's currently taking, and questions about her period, depending on her age, time she stopped, and all things related to that. The doctor might discuss the kinds of shoes she wears, what job she does, and how much exercise and what kind, and how often she does it. For the physical assessment he will probably do ROM, or range of motion. He will want to check active and passive ROM, as well as her flexability. Depending on how complete he is, time he has, or what he might think is the diagnosis, he might ask her to stand on the floor, arms at her side relaxed and he might check for symetry of her hips, shoulder blades, and shoulders. If one side is lower than the other, it could be that she has one leg shorter than the other which could be the cause of her hip and lower back pain.
2) No, she would not need to remove any clothes for that. A trained professional can usually tell easily enough through normal clothes, not a winter coat for example, whether or not things are not symetrical.
3) This depends on her doctor in my medical opinion. A lot of GP's for some reason automatically send patients out for things that they can do themselves. (This is one of my soapboxes, sorry). A GP is quite capable of doing a complete gyn exam and diagnosing gyn issues. Now anything major, yes, a patient needs to be sent to the gyn, or respective field. There are 1001 possible diagnosis' for irregular vaginal bleeding, everything from scratching an inner wall with your fingernail while inserting a tampon or toy to way more seriuos things. A GP can probably diagnosis a good 90 percent of what's wrong, and of the remaining 10 percent is pretty sure he know's what's wrong with about 50 percent of that. But nobody wants a lawsuit, so better go see the specialist. He is sending her for a vaginal ultrasound so the the gyn will already have the results in hand when she goes. It will greatly assist the gyn in maybe being able to make a quick and accurate diagnosis. He can trouble shoot from there. As to whether the Doc does a pelvic or not depends on the doc and what he thinks the diagnosis might actually be. I am guessing he did a rectal for 2 very simple reasons. One, you would be very surprised how many people come in complaining of vaginal bleeding when actually they have an internal hemorrhoid and they can't figure out which hole the blood is coming from. And in their mind, a vagina bleeds every month, butthole don't and shouldn't. So most just assume it's vaginal blood. So first of all, the doctor probably did a rectal exam to determine that in fact the blood was vaginal and not rectal. Once he determines where the blood is coming from he will know what he either needs to do next, or who to send her to, the gyn for vaginal bleeding, or the GI doc for rectal bleeding. Once in there he will also be checking for any gross abnormalities or hemohrroids that might be causing the bleeding, or might cause future issues. Once the determines where the blood is coming from, he has no need to examine any further unless he thinks it's a diagnosis he can fix.
4) A lot of table have completely hidden stirrups, not always, but sometimes. A lot of offices have a special gyn chair in the special gyn room and you have to have a badge and know the secret pass word to gain access to that room, lol, just kidding. But seriously, many doctors offices only do gyn exams in one special room. If the table is up against the wall, she could bend her legs as in frog leg position, leaning one leg up against the wall. That should still give the doc ample room to see what he needs to, or have a feel inside. Or he could have her lay on her side facing the wall and pull her knees up to her chest and he could do a vaginal exam from the back. I have examined many of my patients in this position and for the exact same reasons as your wife.
5) It sounds like your doctor is a bit Republican, errr, I mean conservative, so I am guessing he didn't put her in knee/chest up on the table, although it is a very acceptable position, but a tad embarrassing for the patient. He also could have her standing and leaning over the table, the same position many doctors put their male patients in for their DRE's, and or prostate check, but I highly doubt that either. Most likely he had her on her side facing the wall with her knees brought up to her chest.
6) Could be, could be not, depends on how your doctor wants it done.
7) Also, again depending on how formal your doctor is or isn't might depend on a coverning or not. By the sounds of it your doctor sends many patients out to specialists, that's his mind set. And because that's probably his mind set, he only needs to do a very quick visual and in and out in a few seconds and he's done. It would take 5 minutes to get her pants down, in position, gloves on, and patient properly covered and only 30 seconds for her to lower her pants to the tops of her legs while the doctor dons his gloves, applies lube and gets in and out. He's only going to see her bottom if she's laying on her side. And with a drape he would be pulling it back far enough to expose what he needed to see, which would be the same amount he is going to see without the drape. Make sense? She doesn't need to take her pants off for the exam I am guessing he performed.
Hope this helps answer some of your thoughts and or questions. And remember, I am just a nurse, I am not a doctor. I am only telling you what I know from either experience, or from talking to my boyfriend who is a real doc, or from what makes sense medically speaking from my little knowledge of human anatomy, body processes, and forming of diagnosis'.
Mashie