R. Loew was a smart guy and he already thought this way. But he knows he couldn't completly rewrite the windows (esp. without sources) so he rather created specialized SDKs for multiprocessing and for using memory beyond 4GB, it's listed in his software site:
MULTCORE: SDK to support Multiple Cores.
MEMORY64: 64-Bit Memory SDK for Visual C++.
This would enable the developers, who for some reason needs still run on W98, to write theirs SW to utilize this modern HW capabilities with his SDK. But I never seen a public available app that would use his SDK. Unfortunatelly after his death this SDKs was not found/published yet... but probably nobody would put effort in it even if available...
Gigabyte GA-P67-DS3-B3, Core i7-2600K @4,5GHz, 8GB DDR3, 128GB SSD, GTX970(GF7900GT), SB Audigy + YMF724F + DreamBlaster combo + LPC2ISA