Is this sentence grammatically correct??

Yes. My only change:

I had to not only calculate the structure but to also develop an entire report and draw the proper diagrams and figures using different software like Catia V5.

Is this sentence grammatically correct??

I had to not only calculate the structure but to develop an entire report and draw the proper diagrams and figures using different software like Catia V5.

Not only must I design the structure but to write an entire report with proper diagramming using different software such as Catia V5.

I suggest:

I had not only had to calculate the structure but also had to develop an entire report and draw the proper diagrams and figures using different software like Catia V5.

an entire report ... indefinite article

proper diagrams ... plural indefinite (without article) 

Is this sentence grammatically correct??

I had to not only calculate the structure but to develop an entire report and draw the proper diagrams and figures using different software like Catia V5.

Grammar is ok. However I prefer to avoid the negative forms like 'Not only' and use something like 'In addition to calculating ... I had to ...'  ... and yet 'Not only ... but... ' is really perfectly ok.