I should have reviewed the code in the comment phase, but anyway:
1) There are still some coding style issues, e.g. indention should be four spaces, no space after not (!) operator.
2) The file HL7.php doesn't make any sense to me. If the values you set there are really configurable, they should be passed as parameters to the according class constructors. If not, they should be defined as constants. As the file doesn't contain any code, only variable definition, it should be ditched completely. Even better: define a Net_HL7 class there to retrieve objects defined by your package.
3) There are two empty classed that don't make any sense to me: Net_HL7_Request and Net_HL7_Response