A good way to compare costs for new units is to create a few standard units in the #UNITS section, one similar to the one you are creating but with legal limit of two abilities, and a few humdrum ones like armored speeders, infantry with a few goodies, that sort of thing, just as a testing benchmark. Then create your new test unit as well. Make sure the number under #UNITS represents the correct numner of units there.
Then go into the game, call up a new game, then look in the help section of standard units or something like that. Each unit will have its final cost in minerals displayed. Again, whatever you hardcode/assign as cost of your unit, the real mineral cost that will show in the help will be x9. So, say you want your unit to cost the equiv of a benchmark test unit you made up earlier, say a Photon Speeder. Take the cost indicated in the help screen for that example unit, divide by nine, and that's the number you put in alpha.txt for your newly created unit.
Bear in mind that for every change in #UNITS, all saved games using new units will be associated with the old #UNITS version, as it appears the game file records the #UNITS in it. So trying to test a new unit with an existing saved game might cause you problems, like units not showing up on screen or in the help files, abilities and costs being wrong or units subing for other units. So every time you test a new configuration of #UNITS, no matter how small the change, load up a new game -- then just use ctrl-k to test the unit, shift-f1 to place units to pit them in test conditions against one another.