Boot time significantly Increased

Hello Guy and Gals , My system used to boot up Quite Fast ( almost instantly SSD Drive C ), i added a hard drive and noticed a significant increase in my boot up time , the drive i added , i decided that i would not use it ( Not Big Enough ), so i removed it,

I then noticed that my Boot time increased Significantly ( not almost instantly before i added the HD) i went to my disk management and checked my hard Drives and it asked me if i wanted to initialize disk 0 ?

The only Drive i am concerned with is the SSD Drive which is labeled C:\ in disk management that is where my OS is sitting , ( and also disk 1 ? ) i was given a prompt with the Default option GPT GUID partition table

i am not sure if i should go with the Default option ? and would choosing that option revert my C Drive to the Fast boot up time it had Previous to adding the HD ? any help would be appreciated

Thanks in Advance

Also i just found out that i have a whole HD missing , the was in 3 Partitions ... not looking good