It has been a while since the last time I simulated trees with EPIC or APEX but I think I can still give you some information.
To remove branches, I remember I modified a harvest operation. The concept is that you want to remove biomass from the plant so, you can create a new harvest operation with an override harvest index greater than 0 (in this way the model knows that the operation is meant to remove biomass). See the user manual for the definition of the override harvest index. You will have to play a little to find a good value for this variable. Then, you want to set the tillage depth to a large negative value (for instance -1500) to tell the model that the operation occurs above the soil surface. The last modification I can think of is how you want to treat/simulate the reside of the pruning operation. If you want to simulate that the residues are removed from the field, you want to set the harvest efficiency at one (in this way all the harvested/pruned biomass is actually collected) while, if you need to simulate that the residues remain in the field, you want to set the harvest efficiency to a very low value. You can check if the residues are removed or not from the field by looking at the residues in the output files.
There is not a specific operation to harvest grape but, again, you can create one. You want to have a negative tillage depth, harvest efficiency equal or close to one, while the harvest index is set in the crop table (so, in the tillage table you will have to set the override harvest index at zero).
For the management file, if you have operations that occur every year on the same day, you can create a management with only one year and in the harvest operation, you will have to specify the time from planting to harvest when you create the harvest operation. The only thing I am not sure about is if, in this way, the harvest operation will occur every year after the first harvest operation or not. Please give it a try. If you have operations that occur only in some years, I think you will have to create a management file that covers the time the trees are growing.
I can't remember if, in the special case of trees, you can skip years in the management file. As I said, it is a while since the last time I simulate trees with the model and I apologize if I don't remember some parts now.
Please, try to create a management file that fits your needs, and do not hesitate to contact me again if you need help.