*NOTE* I've stopped working on this CPU now and started work on a newer CPU with many more functions which can be found *here*. If you are actually interested in this older model, you might be better off looking at the latest revision available *here*, which has a number of improvements over this version. However, if you are just looking for a Minecraft Computer to play with or inspire your own build, you'd be much better looking at the Mk2 in the first link, it's far superior to this CPU.
This is version 4 of my Minecraft CPU, which includes all written in the title, fixes for the bugs in version 3 (mostly memory controller problems, this should work now :D), and a few other optimisations here and there. I've also developed a new memory cell, which can be stacked one block closer than the previous version, and is 1 tick faster at reading data into the cell. The RAM has been rebuilt with this, but there is far too much ROM for me to bother, and the gains aren't that great considering the read time doesn't matter for that, since it wont be changed during runtime (or at least shouldn't be :P)
Another change which makes no difference to usability yet is the addition of a proper decoder for the control bits, rather than each of the 3 rightmost bits being dedicated to a task, they are now properly sorted to allow for the maximum number of instructions. of course, I haven't found anything to do with the new ones yet, but I'm sure there will be something. the new design makes the memory controller 1 tick slower, makes no change to the commands you give (so they are still write, clear and read respectively, reading right to left), but I've added a clear and write function (untested yet, great aren't I?) which is set to 011.
Other than that, I don't think anything else has changed. I haven't been playing Minecraft as much as I used to, so development has gotten a little sporadic, and I haven't been logging as thoroughly :( So, if you find something in this version which doesn't work as it did in the previous version, or doesn't work at all, please let me know in the comments. Other forms of criticism, suggestions and complements are also very welcome :)