Why does my 93 saturn sl2 kind of hesitate when i shift gears?

i have a 5 speed 93 saturn sl2 with about 145,000 miles on it. i love it but it runs ruff. when i shift between gears it kind of hesitates or cuts out only for a second, i have no problem getting into gear it just kind of chokes between shifting. It is also blowing black smoke out of the exhaust, and the spark plugs had oil and gas mixture on the bottom of the plugs last time a changed them which was about 2 weeks ago. since then ive replaced the egr valve, coolant and air temp sensors and o2 sensor. it has improved but it is still blowing out black smoke and hesitating between shifting. also if im idling for more then a few seconds, when i press the gas it cuts out for a second and then usually kicks in but sometimes it stalls. thanks