I presume the manufacturing ISO 9001 certificate scope excludes design? If not, you should be part of their management system. If design is indeed excluded there is no specific requirement that you have ISO 9001 as the research department.
Most important question is what the customer wants in this case. If a customer actually reads the certificate the manufacturing site sends them, they might figure that design is not included, and might find it a bit odd.
I don't know a thing about ISO13485, so no help there.
And finally, CE marking: check this website
http://www.newapproach.org/Directives/DirectiveList.asp
It says medical devices need to comply with the following European guidelines. These guidelines will explain what is required for EC marking for these specific product groups. There is a specific guideline on applying the markings themselves.
90/385/EEC Medical devices: Active implantable
93/42/EEC Medical devices: General
98/79/EC Medical devices: In vitro diagnostic
There might be other guidelines that apply to your product as well, low-voltage equipment, machinery guideline, etc.. This website might also prove useful:
http://www.conformance.co.uk/directives/ce_list.php
regards, Martijn