Yes, in a case like this you have to make your best estimation of the amount that was paid. Since you have the gross and net amounts, you should be able to get pretty close.
The employee's Social Security is withheld at .062 and Medicare is .0145.
Say the gross is $500 for one week, and the net is $425.
Total tax withheld is $500 - $425 = $75.00.
Social Security tax is $500 x 0.062 = $31.00
Medicare tax is $500 x 0.0145 = $7.25
Federal tax withheld is $75.00 - 31.00 - 7.25 = $36.75
You can't efile with a Form 4852. You are supposed to include the amount on your original return, then print and mail it in.
Some people e-file their return and leave their Form 4852 off, then amend the return later to add the Form 4852.
If you live in a state with a state income tax, you can complain to your state Department of Revenue. Check here for contact info.
You can complain to the Department of Labor. Follow this link for more about that.
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