I need to move a toilet to the other side of room approx. 6 ft I will have to drill a 3.5 in hole for the waste line in 5 floor joist on the second floor. Can I double them and still drill the 3.5 in hole and be in compliance?
You need to box off that floor joist. You can remove an section of the joist in the way. You then build a box connecting the ends of the cut off joist to adjacent joists with perpendicular ties of the same dimensions of lumber. 2X10's for example. These ties transfer the load to the adjacent joists and give you an opening for plumbing or duct work.
Not unless they are 2x12 floor joists and it goes exactly through the center. The maximum permissible boring in a floor joist is limited to 1/3 of the height of the joist (with a 2" minimum). See IBC 2308.8.2.
Sistering the joists would not effect this restriction, as it is an issue of the structural integrity of the framing member - not an issue of the required lumber dimension for a given span.
Simply following building code, you'll only be allowed to bore a 3 5/64" hole through a 2x10 joist. A 2x10 is actually only 9 1/4" deep, and building codes set the maximum hole size to 1/3 the depth of the member (9 1/4" / 3 = 3.08333").
If it was only a joist or two, boxing off the section might work. Using this approach for 5 joists, may or may not be the best way to go.
Another option, is to consult an Engineer. The Engineer will be able to provide a solution, and will include all the documentation required for the solution to pass inspection.
NOTE: While the above image was a solution designed by an engineer, it is not a solution that will work in all situations. This solution will not pass inspection without the proper documentation.