you shouldnt notice any issues if the holes are small. But be sure to fill them in when you finish the box. maybe fill them with some bondo for now. It looks pretty good.
I dont know if its been mentioned already but heres a small tip I learned that will help you out a ton:
Get a 1/4" roundover bit or even a rabbeting bit for you router and cut a groove around you edges and your sub rings that you can staple your fabric into. For the roundover bit you just set it deeper than you nornally would for a smooth round edge. It makes a stepped roundover. Once you resin the fabric you can use bondo-glass to build up the transition between the fabric and the mdf. It keeps your nice clean edges from your mdf cuts. Also, cover the bare mdf with painters tape where the fabric meets it and you wont have to sand bondo off of the wood. Doing it this way also keeps you from sanding through your fabric where you stapled it. I can try to do an illustration in MS paint if I didnt explain that well enough.
I'm glad it turned out good for you. I wish I would have seen ur post sooner so I could offer more help. Fiberglassforums.com is also a really helpful site with a lot of cool people u may want to check that out. Lemme know if u got any more questions and ill see if I can help. FG is one of the few things I know a lil about. Good luck.
Are the 6x9s in the package shelf? If so you could build you up some spacers out of mdf. 2 Layers of 3/4 will give you 1.5".
I say just build a strong front stage and eliminate the rear speakers.
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Well this thread inspired me to finally start my stereo build in my car