We prefer 99.  The Lakes in Chowchilla was very nice when we were there about a decade ago.  The town is not.  Bakersfield has a number of good parks.  The two previously mentioned rest stops were closed last week when we drove thru.  As far as 5 goes, Almond Tree & Kitt Fox are ok for overnighting.  We frequent Flag City.  It's Passport America weekdays I believe.  We've stayed at Expo, prefer Mark J.  It's adults only.  Check reviews at one of the RV park review websites.
Both 5 & 99 have horribly rough road conditions in places.  Around Stockton on 5 was absolutely the worst when we traveled it last Fall.