Get as much of the silicone off with a razor as you can then sand the acrylic. You are most likely going to sand and polish the acrylic once you are done welding the tank back together so you might as well start the sanding / polishing while it is apart (much easier than when the tank is together!).
I would start at about 1000 grit sand paper then 1500, then 2000, then Novus polish. If you do this for each acrylic sheet you will be pretty much assured that there is no silicone residue left on the surface.
I do not know if you want the weld surfaces polished out with the Novus polish when welding the tank??? I would think that you would want a little bit of roughness to the surface to get a good bite with the weldon... but I have never built an acrylic tank so take my advice for what it is worth. I HAVE done plenty of polishing on acrylic tanks though!
If it were me I would polish the whole acrylic sheet down to the fine Novus. Then mask off the non-contact points of the tank with masking tape and scuff the weld contact points of the acrylic with 1500 grit. The 1500 grit surface should give you a better bond than perfectly polished acrylic.
The only time silicone will stick really well to acrylic... is when you don't want it on the acrylic!