首先,could是can的过去时.
I can swim.I could swim.一个只表示现在会游泳,一个只表示过去会游泳.
I thought I could do.vs.I think I can do.
这里的can表达的是一种能力,能够.
其次,I could have done it.表达的是一种推论,对过去发生的事的否定推论.
He is so honest that he can't have stolen your money yesterday.他那么老实,不可能昨天偷你的钱.
再次,严格来说,单个的I thought I could have done it并不能表示它是一种虚拟语气,它只是表达一种推测,一种可能.因为虚拟语气表达的一定是相反的情况.I thought I could have done it只是一种推测.也可能做了,也可能没做.而如果是虚拟语气：If I had arrived earlier,I thought I could have done it.我如果早到,我就可以做做这件事了.（事实是没有早到,事情没做成）