I wouldnt use any thread tape or gasket sealant when you put the boiler back in, for the exact reason you found out. Little bits of it will drop into the boiler and end up heck knows where.
As long as the threads and flanges of the pipes are in good condition (no pitting or scoring) everything should seal up no problem.
Good work on the tear down, its a really nicely put together machine. Im kinda wishing I snapped it up now :)