I am about to fit FP velocity stacks, decat Y-piece, and BMC race filter. Do I need to re-map my PC3 (currently on base map) or can it wait til I do the slip on mod??? Is there anyone with a map for this set up on a European model (different I think from the US model). Thanks.

It can waite untill you install your slipons. It won't hurt anything. Do your mods and then dyno tune to save yourself some money. Sorry, I don't have a map for what your doing.

I'm interested in a map for this setup as this is what I'm installing soon.

Redlion, how much of a difference did the Power Commander make to slow speed riding like pulling away from lights or doing a constant 30 - 40 MPH?

This is my only gripe about my bone stock 04 R1 as the throttle seems really on off and not always that responsive when riding at slow speed.

Hi IK, I would definitely recommend fitting a PC3, you are going to need one in any case if you do the mods you say and change your cans. Personally I do very little low speed riding as I ride solely for pleasure and mostly on empty European back roads (I came from a litre V-twin Aprilia sports, so you want to try one of those for pulling away and round town if you want to know what hard is), however even with just the base map there is a substantial improvement. I found the bike ran considerably smoother particularly low down where it will help with your 30 - 40mph and mid range. Probably also made a difference to the top end too but to be honest above 9.5 - 10k its so mental anyway I probably wouldn't notice. Power and torque in the mid range also felt a little stronger, and fuel economy improved by 5 - 10 mls to light on, which is a bonus for me as I am mostly doing 400+ mile days. Without custom mapping it will provide you with 'nearly' optimised fueling which is a considerable improvement over a stock bike.
For me I would want to have the PC3 even on a bone stock bike, and then be able to custom map at a point when the performance mods have been done. For what it is worth PDM Racing reckon that a custom map will make an appreciable difference on a stock bike from the PC3 base map.
Still like to find a map for the velocity stack, de-cat and race air filter set up though.