Just replaced a master cylinder with a different type and it turns out that the new one has a slightly longer push-rod, hence the bias bar is now quite a way off parallel (to the bulkhead) under normal braking load. Otherwise everything seems fine.

How critical is this, do I need to trim the push-rod down or is this OK?

You have to make sure it's not binding at the edges, and if it's too far out of parallel, you won't get proper effort in both circuits - there are a few guides on the web, here's one:
https://www.merlinmotorsport.co.uk/images/brakeclutchpartsl/Merlin%20Motorsport%20OBP.pdf

You have to make sure it's not binding at the edges, and if it's too far out of parallel, you won't get proper effort in both circuits - there are a few guides on the web, here's one:
https://www.merlinmotorsport.co.uk/images/brakeclutchpartsl/Merlin%20Motorsport%20OBP.pdf

id assume your brakes are no longer balanced. Follow this guide or get them set up before heavy braking.

https://obpltd.wordpress.com/2010/07/30/how-to-set-up-a-race-pedal-box-bias-bar-tech-session/

It's not binding at any point and I'm aware I will need to adjust the bias before using them.

Not sure what you mean by "not getting proper effect in both circuits"?

Decided I wasn't happy with it so took the master cylinder out and trimmed 1cm off the push rod. Nice and straight now. I guess if nothing else I have saved myself 4.3 grams...

[Edited on 7/5/15 by rodgling]