No you don't have to take everything out (I know you're really asking about the stretch bolts to the motor mounts.)
If you don't have VAG-COM, you're going to need to get with someone who does.
Make sure the motor is warm first, saves you time. Just remove the top TB cover, and adjust the timing by loosening the 3 13mm bolts to the fuel pump sprocket and then with a 22mm 45degree offset wrench (hey it worked really well for me) roll the injection pump in a clockwise direction (this causes the sproket to move in a counter-clockwise direction relative to the fuel injection pump.) I can't tell you how far you need to go, since at this point it winds up being a trial and error adjustment. Once you think you might be in the right zone, tighten the 3 bolts, remove any tools that might be in the way and start her up, verify the timing with VAGCOM. I like mine at 65 (Block 2) and 110 (Block 9). DBW recommends 70 and 110, if I remember correctly.
That's the first thing I'd do... However, I also have a vintage BMW and I like to know if I'm at TDC when I'm suppose to be, so if the problem persisted after the above adjustment, I'd also verify that the crank and the cam shafts are at TDC when they are suppose to be. This requires the tool kit (and don't forget to lock the injection pump if you have to slacken the TB - prevents slippage and more headaches.)