You can get all things done in Colon, but here are instructions how to get it done in Panama City (reserve one day for this):

– First thing you need to do is to get your bike inspected. You can get it done in N 08°57.998’ W 79°32.697′. Go there in the morning at 8am (red door). They stop doing inspections at 11am. You need to have a copy of your passport, title and Panama customs form.

– After inspection is done you need to wait till around 2pm, before you go to DIJ office in N 08°57.914’ W 79°32.720’. There you can pass long queue, give your driver´s license to the guy in the booth (he will give you a visitor pass), you just tell him “secretario general” or something similar :). Go in, give your passport to the front desk and wait. At some point someone will ask you to fill a form (you need to give copies of passport, title, customs form and drivers license) and then you wait some more… Finally, you will get a DIJ document. Without this document you cannot buy ferry ticket (from Ferry Xpress office in Panama and you are not allowed to board the ferry in Colon).
– Now you can ride to Ferry Xpress office in N 08°58.502’ W 79°31.040’. There you need to hand over copies of your passport, title, customs form, DIJ document, driver´s licence and Panama insurance paper (they can make copies there free of charge). Ferry ticket was $279 (with reclining seat). Cash payment only.

I stayed in Voyager International Hostel in N 08°57.230’ W 79°33.317’. It is cheap and close to DIJ.