Hi, good for you for removing the pebbles. Now is the perfect time to repot an evergreen conifer (rePLANTing is only for in-ground trees :-) and do keep yourself from watering that poor thing until more-than-less of it's now til you do repot. Deciduous trees should wait til spring except for maples, which you'd do as late in the fall as you dare before the soil freezes. BTW, I'm from Mtl. and I don't think you're zone 3, 4 maybe depending on where you live, but in any case it's still too cold for a small juniper in a pot just to live outside like that. Do get a much larger container of mulch and bury the pot and mulch over the top by 1-2". Keep the container in the shed and don't water at all once the soil of the rootball freezes. I might move the container from the shed in late Feb. so it begins to get sun, and I don't think the window option leaves enough room for enough mulch for protection, so the shed is probably best. When you repot now, use mostly grit depending on what's available - I always tell people to get aquarium gravel in a natural color because it's easily available, looks good and comes in different sizes. Mix it (it should be 75-80% of the mix) with pine or fir bark mulch in small bits (not always easy to find but you can use repti-bark from the aquarium store or soft and break-up-able bark from a bag of Schultz Orchid mix), and some coarse soil from a nursery that isn't mostly peat, or replace it with perlite. Worst thing you can do is to un-mulch it in spring before the last frost of the season - usually around May 1st is safe - because even if things thaw prior to then, if they freeze again the tree can die as tiny new growth will be killed. SO... anything else?

Thanks Lucy, you are of great help. I will repot asap as per your suggestion. Thanks as well for the zone tip, I was going by the map provided by this site but I have to say it isn't a very good reference, very difficult to get an accurate read.
Much obliged!