Well ... I don't know about removing a pane. I know pro tank builders do that sort of thing. When I tried it once on a 20g it was pretty much a disaster, I couldn't cut the silicone at all and ended up having to use a hammer to remove the pane that was coming off. So it can be done, just not by me apparently
Depends on the size of the holes you have drilled, but if they're 1" sched-40 bulkheads they're probably 1 - 3/4" diameter. Unfortunately with that size hole you don't have a lot of move up room. You'd probably even not be able to get sched-80 bulkheads in there.
You could use 1.5" piping and just use bushings on the bulkheads. The bulkheads will restrict the flow a little, but it wouldn't be as bad as say using 1" piping all the way.
You could try drilling the holes out larger ... that is probably not too hard assuming you have access to cutting tools. Jayson probably has everything you need assuming your tank is in Manitoba ....
Or you could go with all new holes, and either silicone a patch over the holes for the 1" or just get a threaded PVC plug and cap them off .. or use them for some other thing (a closed loop or something .. ?)
Anyhow hope there are some ideas in there to help you think about it ...