I'm pretty sure most of us never get back dollar-wise what we put into these old bikes. I think we get back more in the way of satisfaction and enjoyment from their use. Are you saying you don't plan to keep the spare engine? Seems to me it was pretty handy to have on hand considering your current situation. I have a spare engine as well that I've been meaning to rebuild so I could swap it in while I re-do the original again. I just never got around to it, lol. But now that my original is coming due for refurb again, I'm going to have to get on this, lol. The spare engine came from a $50 parts bike that was pretty beat, so I wouldn't trust just sticking it in there without going through it first.
Let's face it, any hobby is going to cost you some money. As far as motorcycles go though, I feel the 650 can be a very economical choice if you do most of the work yourself. They made near half a million of the things so used spare stuff is still pretty readily available for not too much money. Granted, many of the parts need some TLC and refurbing, but for me that's part of the fun. If I wanted something I could just put gas in and go, I'd buy a new bike. But there really aren't many new bikes that appeal to me, although that new Royal Enfield 650 has attracted me some (I even test drove one).