If all cylinders are firing smoothly, then you have a problem with the clutch. A worn and dirty clutch will make a shuddering feeling as you accelerate, and will continue to do so at any throttle input if in really poor condition. It will seem that the power is really down also.
If you aren't really careful when you put a clutch in you can contaminate it with grease from the pilot bushing, from your hands, etc. You need to make sure to use plenty of brake cleaner/laquer thinner/etc. to make sure the surfaces are clean. If there is any bluing on the pressure plate or the flywheel, they HAVE TO BE RESURFACED otherwise the clutch will slip.
