Stuttering in Multitrack Project - pursuing a solution

Working on 30 min DV project - sent to multitrack from FCP
On a G5 dual 2gh - 2.5 ram - 2nd internal hard drive for media - Soundtrack Pro 1.03 - OSX 10.4.5 - Quicktime 7.0.3 - m-audio firewire solo
The number of tracks I am using is 25 and at the moment they play fine.
The problem with stuttering for me revolves around clips that have been worked on in the waveform editor - removing clicks, hum, noise reduction. The clip that I am working on will play (after saving using reference) in the mix window perfectly. But previous clips that have been worked on will stutter.
And, Bounce realtime to action is not highlighted - so no need or can't pursue that course -- thought maybe would work like audio mixdown for FCP.
Have read many other posts with if not the same but similar problems. Are we facing a software or hardware problem?
Have repaired permisions - deleted preferences etc. - no change
Have had wicked crashes with too many tabs open. Have read other such posts.
Questions?
Is this hardware--
Do I need more ram?
Do I need a raid drive set up?
Do I need a third empty drive for scratch (as works to make photoshop with huge files behave)?
Or are there some setup or software tricks?
Is this project too long for Soundtrack Pro?
Has anyone had this work for them out there?
Called apple support - but they want $200-799 to answer question - eventhough I just got program. They consider this an advanced problem for Pro Support and only will deal with getting program "working".
Please help - if anyone has a working solution for this - it would a great use for many Soundtrack Pro users to find a set up or working process in which this could happen.
The only work around I can think of is to work in FCP and send the files to wave editor from there. Then do final mix in Soundtrack Pro.
Has anyone had any luck?
Cy
G5 dual Mac OS X (10.4.5)

Thanks Collin - a solution seems to have been arrived at.
The program was corrupted with space designer not working correctly.
(exporting with space designer - tested on a new small project - showed that it caused a huge increase in reverb than what was heard on system)
Also M-audio firewire solo seems to not cause problems.
Now for the fix.
Using your advice, I now use space designer on a bus - because when used on a track that contains clips that have been worked on in the waveform editor to remove clicks and/or noise ( and especially more than one track), that clip will stutter - at least in large projects.
The re-install of the program did not go smoothly - apple helped me succeed at this. When re-installing - the culprit - space designer's presets and IR (impulse response) files did not appear on re-install. (saw on this board another person with similar issue) The problem was problaly caused by me - I removed the IR's thinking they could be corrupt. WARNING - If one does this, there is almost no way to re-install the program without wiping the hard disk clean. Apple helped in a work around by emailing me the missing file - and the program got up and going. I was recommended to do a complete hard drive wipe and re-install - haven't done it yet - probably should - but all seems to work okay. This seems to me more than a bit of a problem because what if the IR's do get corrupt and need to be replaced - then one must wipe the hard disk clean and start over? This is going to come up - especially since I see interesting 3rd part IR's on the web.
And, effects can not be placed in tracks, busses, and master out - in any manner on chooses. Soundtrack pro seems to work only when following "standard" audio effect placement.
FOR LARGER PROJECTS
a working proceedure for effect placement
TRACK based effects - are compressors, noise gate, EQ, and delay, chorusing or flanging
BUS based effects - are reverbs
MASTERING OUTPUT based effects - maximizers, warmers, c4 multiband
It would be great if an audio pro post on this board - a standard working process on the use of effects - it would be great since not using them in a standard order seems to give alot of the issues that I have read about.
Not answered on this or any board is
Best Hardware Setup - should be a new thread -
Does Soundtrack Pro benefit from/play best with--
more that 2.5 gig ram--
raid drive--
certain sound cards--
certain midi devices--
G5 dual Mac OS X (10.4.5)
G5 dual Mac OS X (10.4.5)

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