Upon leaving my company, can I rollover 401K "after-tax" contributions to a separate IRA, and then convert that IRA to a Roth IRA, without a tax liability. It appears that according to Tax Code 408(d)(1) and(2), that I would be able to, but I need calrification.

Your statement "separate IRA" concerns me. If you roll over only the after tax money to an IRA, and you have no other IRAs, your plan should work. But if you roll the entire plan into IRAs, even if the IRAs are separate, then your plan won't work.