Given the fact that there are state routes in California, Oregon and Washington numbered 99, I'd upgrade them all back into US 99. Starting at Calexico, CA (the original starting point), US 99 would follow CA 111 to Palm Springs, and then follow I-10 and CA 60 into Los Angeles. After going through the East L.A. interchange, US 99 would take the Hollywood Freeway (US 101/CA 170) back to I-5. (US 101 could then be rerouted along CA 134 towards Pasadena.) At Mettler, US 99 would replace CA 99 through Bakersfield, Fresno and Sacramento. After another short multiplex with I-5, it would break off again to go into Marysville, Yuba City, Chico and Red Bluff before rejoining I-5. With the exception of CA 273 in Redding and CA 263 in Yreka (both of which would be upgraded), US 99 would be limited-access to Oregon.
US 99 would replace all of OR 99 in the Medford area, and also from Springfield to Junction City. The split routes would be eliminated, with OR 99W becoming US 99 and OR 99E becoming Alt US 99.
In Washington, US 99 would break off I-5 at Centralia, replacing WA 507. Then it would take WA 7 into Tacoma and the Pacific Highway into Fife, where WA 99 currently ends. WA 99 would be upgraded back to US 99 through the Seattle area and on to Everett. A new alignment would be built, continuing northward to Blaine. US 99 would end at the Canadian border, just like it did way back then.