VideoRedo is the current go to product in the HD crowd, but if all your doing is editing out the commercials the latest version of HDTV2MPG is just fine - just dont use it for convering to MPEG (ironically enough) - keep in transport stream mode.
Keep in mind some players are very sensitive to faults in the files. I find that while ZoomPlayer/TheaterTek are the best pictures that between Media Player Classic and VLC you can play just about any file. <aside>For 1080i I cannot recommend more the Zoomplayer DScaler5 combination with an external library by a guy named kezuh (sp??) specifically for 3:2 pulldown on Film 1080i files. <aside>
mpeg2repair will not work magic, and it can be inconsistent, i.e. some folks find occassionally that the repairs are worse than the original, but I find it usefull.
I'd say that if you find that your Firewire Caps are continually faulty consider the firewire port. I had some issues in the past with the Firewire ports on VIA chipset based MB's and the one on the ATI All-In-Wonders. I spent $20 and bought a four port dedicated PCI Firewire card and haven't had any significant issues since.