I assume that in the above, you are saying that you are wanting...

I assume that in the above, you are saying that you are wanting to transfer your and your partners personal shares into your own SMSF - unlike some who might transfer shares held in their company and transferring those company held shares into their SMSF.

Yes

And a Financial guy has applied to the ATO for the deed etc

The CGT event will be a problem unless something is done in regards to the shares over the next couple of days