It probably has a more closed design on the 50 cylinder head to lilit the flow through the cylinder. As for the 90, do you know if it is a looper or cross-flow. Both were available in 98. If it's a looper I would consider it, but a cross-flow is one thirsty SOB. Upgrading your 50 to a 70 would probably be the cheapest, and then get a good prop. I had a friend with the same PRO-LINE that you have and his had an 85 MERC on it, he felt it was slightly overpowered for him.
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2011 SUNDANCE B20CCR SKIFF, 2011 YAMAHA 90HP 4 STROKE, 2011 KARAVAN SINGLE AXLE ALUMINUM TRAILER, LOWRANCE ELITE-7 HDI, MINN KOTA RIPTIDE TROLLING MOTOR
2000CC HYDRA-SPORT 225+HP EVINRUDE SOLD 
AND THE PINK JEEP!!!! R.I.P.
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