It's hard to tell from your pics what exactly is bypassed, but the
Honeywell wiring diagram looks straightfoward. The thermostat should be
connected to the bottom left and bottom middle terminal. The power
supply should be connected to the bottom left terminal ( along with 1
leg of the T-stat wire) and the bottom right terminal.
Now for the end switch terminals the wiring diagram says it goes to the
circulator. I am assuming it goes to a relay box first which closes the
circuit to activate the aquastat/boiler and circulator. Is that where
the wire goes, to some kind of relay box?