Now the project and margin calculation were in process

...........我语法不好~不敢肯定~但是至少我从来没看过这种时态混乱的句子~

应该是

Now the project and margin calculation are in process/ under processing~

当前项目成本和利润都在核算当中~

最基本的~既然有now在前边~后边就乖乖的用现在时吧~

Now the project and margin calculation were in process

我觉得没有错.
首先这句话表达的是已经做了的动作,时态就是过去时,now无所谓的.
其次,主语是复合主语,所以谓语用复数,也没错.

Now the project and margin calculation are in process