7AFE Runs rough when cold, Until the car gets close to warmed up, the engine runs poorly Options

[GriffGirl]

When I go to start my car, particularly in the morning after it's been sitting all night, the engine feels like it's kind of "chugging" or "hicupping" until it's warmed up. I noticed this right when I bought the car, about 6 weeks ago, and that the temperature gauge was taking forever to go up into the "warm" position.

So naturally, my thermostat must be sticking, right? Well I replaced the thermostat last weekend, and while the car warms up at a normal rate now, it still does this weird "chugging" thing from the time that it begins to warm up until it's about 2/3 of the way to temp.

I did notice that the day after I replaced the thermostat, the car didn't do this. I also noticed that there was a slight leak from where the upper radiator hose goes into the engine block (my fault - I took the wrong thing off in search for the thermostat housing, and didn't use enough sealant when I put the mounting back on). So when I fixed the gasket seal and put everything back together, it resumed it's chugging thing.

Could this be because of air in the line? I'd think it would overheat if there were air though. Bad coolant? It's almost as if there's a vacuum leak, but I can't find one anywhere, and it just seems directly related to the cooling system since the duration that the car does this has also decreased with the proper warm up time in place now.

Any ideas? Thanks!