The other measures should have been taken before the siding was installed.
Flashing a fieldstone chimney along siding.
Proper flashing around a chimney includes two layers.
Sections of l shaped sheet metal are woven into the shingle courses and lapped up the side of the chimney.
Along the bend at both ends so that the flashing bends around the chimney at the bottom and overlaps at the ridge.
I ve looked around a bit and all the details i can find only deal with chimney roof flashing.
Pieces of 18 inch wide flashing installed prior to the brick work but on top of the house wrap in a stepped fashion periodically laying on top of the lapped upper portion of the siding to get the water back to the exterior of the wall is more along the lines that i would be thinking of.
On each end of the pan flashing cut about 1 1 2 in.
A second layer of metal is embedded in the chimney mortar joints and folded down to cover the top of the step flashing.
Once the pan flashing is in place nail it to the roof sheathing and lay the shingles over the flashing.
Yes you can caulk but in reality you should also be using chimney flashing which gets attached to and sealed to the chimney and then gets bent over the j channel.
Next comes the counterflashing.
The first is called step flashing.
Anyplace where the roof plane meets a vertical wall such as a dormer a chimney or a split level roof flashing is necessary.