I like to use FTP and I have not found a FTP client that can limit the traffic during certain time bands.
I would like FTP traffic(port 21) to be throttled/blocked during 8am-5pm, and be unlimited from 5pm-8am.
Is this possible within my Mikrotik RB?
This is possible. Mangle the traffic you want and setup a simple queue for it with the time limitation. See manual for more details. If you are not an IP professional already, you may have trouble understanding the mechanisms of Mangle + Queue.
See examples in WiKi: http://wiki.mikrotik.com/wiki/Bandwidth_Managment_and_Queues ; http://wiki.mikrotik.com/wiki/Limit_Different_Bandwidth_In_Day_and_Night and the new manual: http://wiki.mikrotik.com/wiki/Category:Manual
If you want to save time and effort you should contact a MikroTik certified consultant: http://www.mikrotik.com/consultants.html
Please post your configs here for more help.