I though that might have been the case. When I had the throttle body adapter on mine it stuck out a fair bit but we still managed to get the pipes to fit. Was still annoying and shitty looking though. Took up valuable WMI installation space too.
The only thing that I can see that might bother you with 3 inch piping is throttle lag, and loss of bottom end. Bigger pipes slow the air speed down and make the 2.5L a little sluggish below 3,000rpm. That type of inlet manifold doesn't help either with the bigger runners.
But you installed cams didn't you? If so, what size? That should help. I had a set of 256 Tomei poncams, and they were great. The 3.0L loved them, was really torquey down low.
If I was to go back and do it all again, I would get someone to weld my factory TB straight onto the manifold somehow. I think that would be the best option, but that's just my opinion.
The Q45 will be ok, but might be a bit jerky down low when cracking the throttle. You'll get used to it though. As I said earlier, just remember to fix up/increase the accell enrichment so it doesn't lean/starve.
Its all looking good though, I might drop around one day when you are free and have a look.