This is complicated by the fact that it's a virtual machine and you're not able to take measurements from the hypervisor. You cannot really get good measurements of what's happening at the physical machine level from inside a VM.
It also depends on exactly what you mean by "processes stall." But there are a few things you can look into to at least get you started.
Get Process Explorer, which is like Task Manager on steroids. Run that, and observe how much CPU is consumed by hardware interrupts and DPCs during one of these events. If it's really high (it shouldn't be more than about 5%) then you're looking at a driver issue. You can then inspect the System process and see the CPU usage for every individual thread in the System process. It will usually have the name of a *.sys file in it, and that will be the driver that's causing the issue.
The second tool I would turn to is Xperf. Xperf is an extremely powerful and flexible system profiling tool. It will tell you what is causing the performance problems on your server if you use it right.