It doesn't sound quite right to me. If you do a direct transfer of shares from the 401 to the rollover IRA, it is not a taxable transaction and does not affect the NUA transaction (except where it may violate lump sum rules for 401k's and make the NUA ineligible..not sure on that). If you take the stock out, I don't think you can contribute stock to an IRA, even as a 60 day rollover. I think it has to be cash.
There are a number of web sites around with expert opinions on this, including:
It is not a simple area, and there seems to be some limitations on NUA from 401(k) plans, as opposed to 401a (after tax monies). In particular it looks like a full withdrawal is required for NUA treatment in the case of a 401k, but go ahead and research this carefully yourself. This is quite beyond anything I would consider taking advice from a BB for!