How come my car starts to buck after driving 6 or 7 miles?

How come my 86 Nissan Stanza, 5 speed, manual trans, bucks after driving 6 or 7 miles, especially when driving uphill. The altenator went out last week(I haven't replaced it yet) that's when the bucking started, however it still bucks even with a fully charged battery. It seems to run normal untill it reaches normal operating temperature, and the bucking almost stops as long as I'm in 4th and maintaining 55 mph, and not using lights, wipers, ect., it's most severe in 3rd, and after driving 25 miles to work, my battery is still holding almost a full charge, so could it be the fuel system or timing, Thanks!