OK, not sure if your makerbot still in stock mainboard, I start play with my CTC Dual printer today, I think it is clone of Makerbot replicator dual. and they are really over extruding and noisy. And yes the step motor driver don't have pots on it.
I think I know how to fix the over extrusion issue. So I go to C:\Program Files (x86)\MakerBot\MakerWare\default_configs and find replicatordual.json, you may need to open replicator2x.json for your Makerbot Replicator 2X. And I open the file with notepad++, you can use any text editor to open it. and I changed steps_per_mm for A and B from -96.275 to -88, which greatly reduced the over extrusion problem. I can then fine tune the extrusion by adjust the filament diameter.
I try to search where I can adjust step motor driver current, with no success with any of the keyword I tried, so I went through all code, and find "G130 X20 Y20 A20 B20 (Lower stepper Vrefs while heating)" interesting. It seems like makerbot use G130 to control step motor driver current. So I search all G130 in the document, and found "G130 X127 Y127 A127 B127 (Set Stepper motor Vref to defaults)" under end_start_sequence, so I change it to "G130 X100 Y100 A100 B100 (Set Stepper motor Vref to defaults)", OMG, the noise is so much better, I probably can lower the number further but this already make huge difference.
Keep in mind after you edit this file, you need to restart makerware and redo the slicing, so use a simple model to do the test, otherwise it is going to take long time. I'm not sure 100 is the best value for motor Vref, I need to run more test, but I imagine the best value will be machine specific, so it is best you do your own test.
You can also adjust acceleration (max_speed_change_mm_per_s) and jerk (rate_mm_per_s_sq). I also changed "max_inner_shell_speed": 90, to 40 so that it is same speed as "max_outer_shell_speed". There are also many other setting can be changed, and I'm quite happy with the printers performance after preliminary adjustment.
(Da Vinci 1.0, Jr. 1.0 RAMPS, miniMaker) X4, (Creality CR-10S, CR-10 mini, Ender-3) X4, Anycubic MEGA X4, Anycubic Chrion X1, ADMILAB Gantry X2 (MonoPrice Maker Select V2, Plus, Ultimate)X4--Select mini X1, Anycubic photon X4, Wanhao duplicate D7 X1.
iNSTONE Inventor Pro X2, CTC Dual X2, ANET-A8, Hictop 3DP-11, Solidoodle Press, FLSUN I3 2017X1