Just fit the 044 into the tank, there's a tutorial on how to do it in a 32 gtr on here in the diy section. If you decide to upgrade later go the surge tank and a couple of externally mounted 044's or something more beef I don't think a single 044 is enough to warrant a surge tank and external mounting. I am pretty confident in saying the lines can handle the higher flow rate.
As to the filter, what are the standard ones, i can't remember, have a look around and see what their flow rates are. I would be interested in this if you do find a figure If they don't flow enough just get a aftermarket one and put fitting on it to fit the standard lines and mount in standard location.....can't see there being any probs with that. a good aftermarket one is only about 200 buks and 20bucks for fittings