Not much experience with Molex, but I have used equivalent JSTs quite a bit (VH, XH, PH types etc.). With a bit of care then they are quite easy to solder (as long as you have something that can hold the connector) and a needle-nose plier is then all that is needed to shape the connector to fit in the housing. However, cripting is still a bit easier so on a trip to Japan last year I bought one of these. That will crimp most of these connectors without the need for a dedicated tool per type. Quality is quite good although I can't comment on how long it will last.
//UFN