Hi Rich,
What everyone has said here is absolutely correct, however I'll try to answer you question a little more thouroughly.
The early LA40's had three intake ports in the sleeve and likely produced more all out power than the later ones but were nearly untamable for stunt. In the later 40's OS did away with the boost port and ported it pretty much like the 46. These later 40 can make a reasonable stunt engine and are easier to deal with than the earlier ones. I don't know when the specific dates of anything occurred. The CL versions ("S") came out a couple of years after the RC versions. But of Course, OS had to have their lawyers demand that silly remote needle valve assembly which just adds complexity and reduces reliability for CL.
The 46 with a conventional Needle valve assembly either OS, ST, Or Randy Smith, is hands down the best out of the Box CL stunt engine on the market for under $150.00.
The blue paint on the early engine gave production problems at OS that they eventually got tired of dealing with so they eliminated it. Other than the color it changed nothing.
The 40 went away, I think, simply because the 46 out sold it about 6 to 1, even for the R/C guys. The 46 is more powerful, easier to use, an a little bit lighter due to a thinner sleeve.
I do agree with the comment about simply buying a new 46 unless you can find a used 46 that comes from a known quantity that has been modified (needle valve assembly only) by someone in the stunt community that you can trust, like Randy Smith, or the ones from RSM that are done by Larry Foster.
Everything said above pretty much applies to the LA25 also. They will fly anything that the old Fox 35 was used for and are actually a little more powerful.
Randy Cuberly