Woah, I didn't read this thread over the holiday weekend, and it's really taken off!
I've been attempting for get Minecraft Alpha saves working, but no success so far. It's close (each individual file can be opened bu NBTEdit - a raw Minecraft save file editor), but for some reason the group of files as a whole cannot be opened by either minecraft or two different Minecraft Alpha level editors that I've tried).
If your are spawning in lava, you can try to set the spawn point by placing the cursor in DF, using one of the functions that give the the yellow 'X' cursor such as 'k', or 'v', or 'q'.
However, Minecraft seems to fill the lowest level of the map with lava, so if you are attempting to put the spawn on the bottom of the converted region, that may be the issue. If you don't have the yellow 'X' cursor on screen at all, or if it is an area not included in the output, the spawn defaults to the center of the converted region, on top of the highest non-air block.
As for the number of levels - Minecraft Alpha supports 128 blocks from the bottom of the world to the sky, with sea level being at 64 blocks up. I've been using a similar height in the levels I've been converting for Minecraft Indev.
This means, that you will only be able to get 42 levels from DF into Minecraft Alpha (if I even get it working) as each level in DF becomes 3 layers of cubes in Minecraft (128 / 3 = 42 2/3).
Minecraft Indev can in theory support a much taller level (a few thousand cubes in each direction), but the version that runs from the website is limited to 256MB of RAM, and so it cannot load too large of a level. There is a downloadable version of Indev available from some other sites, but as far as I know, not an official version that is supported.
I'm going to look into the one region that I was sent that crashes DF2MC. Hopefully I can fix the issue. If DF2MC does crash for you, you can use DFunstuck that is comes with StoneSense and other utilities to get DF working again (DF2MC, StoneSense and several other utilities all are based upon DFHack). DFHack allows other programs to pause DF, read from it's memory, and set it going again - StoneSence does this so quickly that you don't notice that DF get paused 5 times a second to read a small section of the level to display, whereas DF2MC pauses it for a longer while and attempts to read all or most of the data from the map. DFunstuck is a small utility from DFHack that undoes the pausing that DFHack does before reading from DF's memory. Anyway, you can use the DFunstuck from Stonesense to get DF going again if DF2MC crashes. If requested, I'll include it in the DF2MC download, but the intention is to have DF2MC operate without crashing, even if it may not be able to do the conversion for some reason, it should leave Dwarf Fortress in an operating state.