I recommend that you jeff's words of wisdom. It will be very easy to start over with a new headgasket at this point, before you hook everything else up. Don't forget to remeasure the bolts for stretch.
I just went through all this with my 300E and it came out beautifully, I hope you have the same experience.
'01 C Class, Six Speed
'84 Euro 240D, manual, 533K miles
'88 300E 5 Speed
'81 300D Daughter's Car
Over 800,000 miles in