IMO, with regards to the deposit and how much it should be, is it should vary with how much of an "oddball" piece you require.
One of the purposes of the deposit should be holding your place "in line".
If you want what is likely going to be one of the more popular configurations(std cam bearings, a fairly normal bore size, std lifter bore spacing and angle), then the deposit should be pretty nominal....... Like $500.
On the other hand, if you want something totally off the wall, then it would seem reasonable to have to pretty much pay most or all of it up front. However.... In that scenario, I would still like to see the $500 deposit in place, to hold your place in line. Then when it came time for your particular block to go through the machining operations that separated it from the "normal" stuff, then you have to pay the balance before those operations take place.