First thing you have to look at is the mountings of the optics. If any mirrors are pinched in thier mountings, you will have problems. It`s often something that beginners do is to make sure that the slightly loose mirror is tightened down well and that causes stress on the mirror. This also means the secondary. Not being familiar with your particular scope, the secondary could be glued onto the holder with a couple of dabs of RTV and that should be good.
Next thing is to make sure that the focuser sees the secondary in the center of it`s axis (a sight tube does the job nicely) and then that the primary is square in the secondary and so forth.
Since the scope worked before you did these things, it should work just as well as before after you get done. The only thing that the low profile focuser should do is to allow a smaller secondary to be used for the same illumination of the FOV which also means the original size secondary will show more of the sky.
Sonotube is a brand name for the round concrete forms made of cardboard. Any construction supply place should have the stuff in stock and it`s not expensive although the tubes that they have may not be long enough for you (they don`t need to pour 20` long posts very often) and it may be that you really want to make a box on the back of the tube to accept a few more inches of travel for the mirror.