1) Inter-story drift limit depends upon type of lateral loading, i.e., wind and seismic. The following two articles explain how to check them for both kind of lateral loading.
http://www.sepakistan.com/topic/1341-ubc-seismic-drift-limits/
http://www.sepakistan.com/topic/109-building-drifts-in-etabs/
Maximum deflection are allowed based on codes too. A Column with axial load and later loading is a beam-column. You can use a limit of L/360 as per UBC for that. This is for local member. For overall structure, you need to satisfy wind and seismic limits. See the links above.
2) Yes it does and no it doesn't. There is a trade off between pinned and fixed support and both have reasons for that e.g., impact on foundation. You as a engineer should value reasons, then analyze the same type in the model and finally make sure your connection is fabricated so that what you idealized is real too. Also, you need to see your framing to see what kind of connection would serve best.
3) To some extent it is what you are saying. If you assume pin, your anchor bolts need to be inside flanges along the webs as you wouldn't develop any moment in base plate. So your base plate wont be that thick. If you go other way, your base plate would be thick with stiffeners and anchor bolts located outside to make that happen. But, assuming pin or fix will have an impact on frame member sizes. It is not just location of anchor bolts. You quantity of steel may bump up if you move from fix to pin and vice versa depending upon framing.
4) Wind should be same for both types. I have done both and my drifts were same. Check your calculation and do a comparison of shears and drifts to see you calculated forces correctly.