The gap in value between those is gradually shifting everyday. Vs. Super Mario has been headed upwards, while Donkey Kong (long overpriced) has been headed downwards.
Figure the Vs. Super Mario to be worth $175 to $300 (depending on condition), and figure the Donkey Kong to be worth $500 (assuming NEW sideart, and used marquee, panel/bezel). Make it $600 if ALL the artwork is repro. Add another $150 to either price if Double Donkey Kong kit is installed.
If the SMB is already really nice, and you are doing it for resale then it probably isn't going to be a profitable endeavour. The board will cost you $100, you'll spend a minimum of $50 more on wiring, no matter which way you go. $20 marquee, $25 bezel, $40 control panel and $30 for sideart means you are looking at a conversion price of around $275+ shipping on parts, maybe $310 total.
Oops, never mind, I just saw you already had board and marquee, that cuts the cost enough where it actually makes sense. You also might just be able to wire yourself a DK to Vs. adaptor and skip the rewiring part.