There's no meaningful clinical evidence that suggests soybean lowers sperm count.
But to be on a safe side consume organic soyabean (not a genetically modified soyabean) to avoid any untowards symptoms.
Next Steps
Try to consume a balanced diet and derive protein requirements from different sources like milk & its products, different kinds of lentils (dals), variety of sprouts (not just soyabean), pulses( like rajma, chole etc), nuts and oil seeds (&/ or non vegetarian food - depending on your preference)
Eating small frequent meals with protein rich mid meals will help you gain muscle
Do follow a proper supervised workout.
As far as muscle gain is concerned consistency is the key - consistency in eating and in maintaining a regular work out regime.
Exercise not only helps you gain muscle, but also helps proper absorption and utilization of nutrients and not to forget makes you feel hungry .
Health Tips
Anything you eat in excess will lead to weight gain ... moderation is the key.
Hope this helps!