Haha--LordSmurf will have a field day with that workflow.
Sounds like you're happy with the miniDV transfers anyway, so you may not want to go through the bother of transferring them again via firewire. Just know that is the intended and most straightforward way to capture miniDV video, since it is already digital.
Your capture card and/or capture app are the likely culprit. Do you have a budget for this project? If so, what is it? We can recommend some stuff you can buy to improve things. With analog video, you should be using line and frame/field time base correctors. Some camcorders have a line TBC built-in--what model camera are you using to play the tapes?
As a first step, you may want to consider picking up a Panasonic DMR-ES10 or ES15 DVD recorder to use as a passthrough device. They're old and long discontinued but are available on ebay. Sort of unique among DVD recorders, they can really clean up a video signal for capture. To be clear, you would not even be using the DVD drive of the ES10/ES15--just passing your signal into and then out of its circuitry en route to your capture card.
TBCs are super expensive and practically unobtanium now, so a DMR-ES10/ES15 is your best bet unless you have a lot of money you can spend.
They also have pretty decent comb filters, so you could *possibly* avoid having to buy a camcorder with S-video output. You would feed the composite signal into the ES10/ES15 and then use its S-video output into your capture box.
Just as an aside, you wouldn't have needed a TBC to do your miniDV captures. Since they originated as a digital signal, they don't have the time base issues inherent in analog tape formats.
OBS is not a good capture app. You should look into whether your card can be used with
VirtualDub or AmarecTV.