so is there any way to do this nice and neat so that you can't tell it was spliced together? or do I do it further up the cable and just tie tape around it?
If you can't swap the pins in and out of the Molex connectors, then yeah, there's a way, but it requires soldering experience and a small supply of shrink-wrap insulation. You can obtain the tools at e.g. RadioShack, but if you're not familiar with their use, then you'll need to spend some time practicing while watching how-to videos on YouTube.
Also recommended: stop by your local home improvement store and pick up an 18 x 18" sand tile and some sick-on felt feet so that you can have a reasonably safe workspace for the soldering.