Is my 2006 Corolla safe to drive for 3-4 months before computer is replaced?

My 2006 Corolla is one that needs the computer replaced. It is shifting VERY harshly. The car is manual and never feels like it is in the right gear. Last night I floored it and it did not accelerate and started to shudder... I had it to the dealership last week, but was told that due to the quake/tsunami, the replacement part will not be in for 3-4 months. I'm understanding of this, but is my car safe to drive for that time period? They tell me it's fine, but I'm not so sure. The ironic thing is, the shifting issue got WORSE after I got the car back from the dealer. I would think they would like to prevent any problems after the brake recall last year...any advice? Anyone having the same problem?