I'm not sure about the crying... Jake cried a few times at nite... and I'd just assume he was in pain and give him some tramadol. But one nite... he woke me up in the middle of the nite with his crying (just softly)... and I jumped off the bed to get to him... I asked him if he wanted to go and pee-pee (he never has to go pee in the middle of the nite), but as soon as I said that he jumped up, so I took him... He actually did a poop instead... then I brought him back to the bedroom and onto his bed... he plopped down and slept the rest of the nite. So I know that time he just had to go (with all the meds and trauma of surgery his schedule was definitely messed up). But the other times... maybe it was just phantom pain ... I don't know. You should mention it to your vet, just in case they think that maybe gabapentin would help (in case it's due to nerve pain).

Hopefully other members will have some good advice for you...

Angel Jake's Mom

Admin, I would tend to think that you are right about phantom pains symptoms, at least from what we have encountered with Oslo's yelping.  Fortunately, gabapentin worked very well on him and he does not yelp anymore. 

But I can kind of relate to what rubyaz has observed with Tasha.  We are still trying to find the cause of that slight moaning Oslo expresses from time to time when he is resting.  A month ago, our vet did a check-up + X-Ray of his remaining front leg.  Nothing standed out. So now we suspect it is a soreness due to his new tripawds walking style…The moaning occurs more often after a good day (which also means longer walks).  But as I said , we are still studying it.