replaced heads

So I neglected my valve clearances too long and threw a couple pushrods a while back. Luckily there wasn't piston damage, but I replaced the heads with new ones as a precaution. I'm currently reassembling the engine but I noticed the intake manifold and the heads don't seem to be lining up...

When i was in the process of replacing my heads i spun the crank shaft pully while distributor and heads were off, am i correct when i say that this messed my timming up?