Yes, go the 39mm route, the 39mm lens boards for the Opemus models 3-5a (and for model 6) are still available new from Fotoimpex in Germany, price is reasonable (around 15 Euros). Alternatively, you might be able to source these parts from nova darkroom in the UK.
Fotoimpex also has some stocks of other Meopta accessories. In case you need anything for your Opemus it might be a good idea to get it while supplies last.
With a 39mm lens board you can choose any of the high quality (6 element) 80mm lenses from the major manufacturers, e.g. Rodagon-S (Rodenstock), Componon-S (Schneider), Nikkor EL (Nikon) etc. These should be availabe for around 50 Euros or so. With the prices for used gear being so low nowadays, I wouldn't settle for any cheaper lens. Make sur you have the right condenser for MF. I am not familiar with the Opemus 3, but usually you have to change some condenser parts to adapt the illumination system to the different formats.
As for the filter question, I am not aware of any pre-fabricated holder for the Opemus. If you don't have a filter drawer in your Opemus it might be easiest to just handhold the filters under the lens while exposing.