lamont:_The Blind Watchmaker_ by Richard Dawkins is still pretty much required reading.
I don't know if it addresses the issues that you're most concerned about directly, though. What you'd probably need would be a statistical analysis of the number of "stable" organisms vs. the number of "transitional" organisms and the chances of them being discovered in the fossil record, along with an underlying statistical basis of genetic mutation which could predict time periods for species to evolve into other species. I don't know of any book that has that kind of information, short of just doing graduate work in genetics...
LOL, the graduate work is out for me at this point.
My current questions at this point might deal with how we identify a transitional organism. For example we seem to see one stage existing for a long time and many fossils found. All of a sudden, they seem to be gone and there's another "stage". In that x number of years we have time for y number of generations yet we have two "stages". To make matters worse, it seems that sometimes the evidence is something like a single tooth or a piece of a skull or whatever. Fossils are hard to make but if we have such solid fossil evidence of two, why none inbetween? In some cases those stages might exist at the same time according to the interpretation of the fossil record. In that case the only apparent explanaition is that they have a common ancestor but in those cases, the fossil record seems even thinner...the ancestor just disappears and the two supposed descendants show up sometimes millions of years later. If it really is understandable that the fossil record have that many holes that are that big, at this point, it looks to me like we need more than fossils. Lacking a direct verifyable connection, it looks to me like a situation where we need to say that we just don't know
I know I'm being kind of general here but that's where my looking is at this point. Maybe I need to pick one single critter and only research that one supposed evolutionary path?