Question 1: Upgrades only! It's essentially the "cost of a frame" since a fresh frame comes with 150k of upgrades! ((That said I've definitely bent this rule once or twice for players that realllllly want that extra starter part))
Question 2: Nope! That SYN comes out of thin air! Harmonizer is an incredibly strong support option!
Question 3: That's a Once Per Allied Phase, so you essentially announce that you're going to redistribute everyone's SYN at some point in the Allied Phase (probably discussed before hand) and whoever opts in is a part of it. Lets say we have 3 players who opt in, Mike (at 4 SYN), Lucy our Harmonizer (at 5 SYN) and Humbaba the Terrible (at 10 SYN). When a redistribution happens you can think of all 19 of that SYN going into one pool and then it can be divided out between players up to their Max SYN.
So maybe Mike gets 12, Lucy takes none and Humbaba holds on to 7. ((Or perhaps if Mike had Unshackled he could get 18)) - The key to using this is knowing / discussing who needs Synergy when singe you can only use it once per allied phase as a free action (unless players want to spend an Action to proc it)
It's a powerful ability that can help funnel dice into someone who needs shields or a DPS getting ready for a huge DMG dump!
Does that answer your questions? ((Happy to clarify anything else you need!))