On vacuum systems I sometimes see bubbles rising from the bottom up to the water level. This indicates a slight air leak at the bottom grommet. A bit of tightening on the lower compression nut stops the bubbles.

When I had a one pipe steam system and serviced the sight glass I would wait around long enough after a call for heat - the minute or thereabouts after shutdown when that system would drop into vacuum briefly - to make sure there were no such bubbles. Also keep in mind you won't see any bubbles if it's the top grommet leaking under vacuum. So if you have a vacuum leak like this and bubbles, probably a good idea to repeat whatever tightening you need to do on both the bottom and top grommets.

Estimated 75' main and dry return. Most of main is 2", last 30 feet reduces to 1 1/4 copper. Pressure gauge needle always rests on the stop.

I've seen these setups work well

for heating the basement... as long as it's full of water and doesn't leak, it's not a problem. 

Will the extra 3-4 inches that the pressuretrol will be sitting higher from it's original position affect its function at all (since it is further away from where it was meant to be originally)?

Aside from not needing to bend over as far to read or adjust it, it will have no other effect. As long as the wires will reach, you're in good shape.

Don't forget to add some water to the new pigtail before you mount the pressuretrol. Are you replacing it with a brass one?