Still bubbling out overflow after changing water pump, thermostat, radiator,hoses??

Ok so I pulled water pump and found a 90%clog in the passenger side port going threw the timing housing!!!. Cleaned it out and flushed block for awhile..put old pump on and ran few times..rremovd pump cause I got a free better one..and put all back together and no bubbling in hoses and not overflowing out radiator ran great..then found thermostat housing leaking so I removed and it wasn't close to flat so I got a All alluminum one and..I'm getting few bubbles out of manifold side of gasket.. guessing the manifold isn't flat..also noticed the intake is getting wet in front seam...so I will be doing intake manifold gasket and getting thermostat surface flat!! Always something...but thanks to all who helped!! And any advice or tech tips for manifold / gasket would help..