volvo 940 rebuild problems/ knocking noise

Hi everyone on the forum, i have a dilema which I am putting out to you all for your advice, I previously posted about my 940 blowing a head gasket, thanks to jockster for the reply, I examined the head to find a crack in the inlet port on No 2 cylinder, scrapped the head. I couldn't get a new head remanufactured anywhere, so I got one from a volvo breakers in huddersfield, it came all complete, looked o.k, measured the surface seemed true enough so i fitted it over christmas. However my problem is that as it took on a lot of water in the sump, I thought that i would spin it over without the plugs in to circulate the new oil, when I do this, there is a knocking sound comming from the engine. I dare not start it incase it goes bang. I set the valve timing with the bottom pulley on the 0 mark and the dot mark on the cam gear in line with the mark on the back of the cover, I have turned it over on the pulley with a socket and after two full turns the marks still line up, I have checked the tappet clearence which range from 11 to 13 thou on them, the shims are there and the buckets all turn round by hand, the only marks that didn't line up were the auxillery shaft ones but it states in the haynes manual not too worry too much as it's only a balance shaft.Has anyone got any ideas please as to what is wrong, is the manual wrong about the aux shaft marks , I am wondering if I have knocked a big end bearing out is this possible, any help will be greatly appreciated, thanks.