I have heard that when upgrading large minster bases this can LAG the server out quite a bit. Perhaps you can add a optional time per piece and then upgrade them one at a time every second or so, The idea is that it would spread all the updates, spawning & special effects out over time vs. calling them all at once.
I'm Assuming you can put wait command within the base objects loop and the setting would be and number from 0 to 5 seconds. Zero would of course not wait and 'do it all'. You could also look at the number of objects that make up the building and upgrade it in subsets like 10 items at a time. This would do small bases instantly and do large bases incrementally over time.
Food for thought ;)