I have a feeling that in another decade, stupid miss information associated with Dana 35 will die off, and it will go up in value.
Dana 35 and 44 share same housing
Dana 35 smaller pumpkin offers better clearance
Dana 35 smaller ring and pinion is not an issue
Dana 35 axle shafts are a weak point that gets replaced in S35 conversion
Downside of upgrading Dana 35 is its price. Parts and regear job will land you $1000 shy of purchasing a complete axle, to your spec, from somewhere like ECGS. Today you may feel good abut saving a grand, in few month you may wonder why didn't you do it.
If you are planning to get Dana 44 from ebay/craigs/fb - i hope you are able to inspect them well.