Here are a few thoughts I have.
You can self certify. This should be low risk since none of the boards are going to be sold or used outside of the company. Here is a quote from the "Export.gov(website)":http://www.export.gov/cemark/eg_main_017287.asp
"Most products covered by New Approach Directives can be self-certified by the manufacturer and do not require the intervention of an EU-authorized testing/certifying company called a notified body. To self-certify, the manufacturer must assess the conformity of the products to the applicable directives and standards. While the use of EU harmonized standards is voluntary in theory, in practice the use of European standards is the best way to meet the requirements of the CE marking directives, especially in the case of the Electromagnetic Compatibility (EMC) and Low Voltage Directives. (The word "harmonized" means that the standards have been approved by all 27 European Union countries). The standards offer specific guidelines and tests to meet safety requirements, while the directives are more general and do not, in most cases, offer detailed specifications on how to meet safety requirements. The Machine Directive, however, does offer more detailed information on how to meet safety requirements than most other CE marking directives. U.S. companies can self-certify to the CE marking requirements of the Machine Directive by meeting the provisions of the directive whether they use European, international or U.S. standards."
"The manufacturer may affix the CE marking to his product once he's prepared a declaration of conformity, the certificate which shows the product conforms to the applicable requirements. He must maintain a technical file to prove conformity. The manufacturer or his authorized representative must be able to provide this certificate together with the technical file at any time, if requested by the appropriate member state authorities."
If in testing your device it appears to be noisy, then look at some fixes, enclosure, circuit changes, etc.. If it is missing an enclosure that can make a big difference and it shouldn't cost much. I remember doing this very thing once for a company and they sent the equipment in a case that was definitely not going to be used in operation, but it was shipped as passing system.