Couple of tricks. Be Human. Thats not only an extra skill point per level, but it opens up the feat Able Learner from Races of Destiny. What Able Learner does is allow you to spend skill points 1:1 for any skill, class or otherwise. That means that basically, once a skill is a class skill, it is forever a class skill.
Second, make Int your highest stat. That means MOAR skill points. Dex and Con and all that can come after Int. Int first! Plus, it fuels your casting, so more spells/day and stronger spells.
Third, look for spells to make up the losses. As I mentioned, Divine Insight is amazing for those skill checks you REALLY need to make. Moment of Prescience is also good, albeit high level. You can also use spells to augment your skills. Why just hide when you can hide AND be invisible as well? Need to create a distraction? Illusions do it bigger and better than anything. Sneak in and cast a Silent Greater Image and pretend that the town is on fire. Most people won't even get a save until its too late.
As far as the negative CL penalty for USS, that's where either Master Spellthief or Practiced Spellcaster come in. They both raise your CL, for the most part. MS sets your CL equal to the sum of your ST and caster levels. Since you can apply effects and abilities in the order that is most beneficial, you take your normal CL, then you put the penalty on it, then you apply MS which changes your CL to a set value. On the other side, you take your CL, you apply MS to set your CL equal to your ST + caster levels, then you apply the Divination bonus. With Practiced Spellcaster, you simply apply PS first. You'll generally have 1 rogue level and 3 CLs lost from Unseen Seer. Thats -4 CLs, effectively. Practiced Spellcaster gives you +4 CLs. If you build with Rogue1/Wiz4/USS10, you'll cast spells as a 14th level wizard with a CL of 15 for non-divinations and 18 for divinations. Simple as that.
Thats one of the main reasons you don't want to lose that many CLs. You get weaker spells (which means less SA dice from Hunter's Eye, or less bonus from Divine Insight, or fewer dice on a SA delivery spell like Orb of Fire or something), and you get fewer spells.
Trust me, if you take Able Learner and focus on Int as a human, you won't have a problem with skill points, especially when you get into Unseen Seer. Sure, you might not have EVERY skill maxed, but you'll have plenty of ranks to go around with your core skills like Hide/Move Silent/Tumble maxed.