I'm running my group through it right now. Had an awesome session last night.
Anyway, I redid the initial encounter with Randel and had the Hobgoblins hassling him on the way to the seven pillared hall. His wagon had broken down, all his ale delivery come to the gate and he has to pick them up himself since their was some "trouble".
After than I had Randel show the PCs around, I printed out the Map from the booklet with a key. And had a few encounters.
Plan out a few encounters and use hooks to get the PCs to visit more places in the Hall, then drop more hooks on them. Hooks, hooks, hooks, use em. Think up ways of having all the PCs backstories matter, have at least one hook from the past show up at some stage or matter to the plot.
So far my group has plowed through the Chamber of Eyes. I changed around a good few of the encounters there, I put in a beholder gauth as the hidden BBEG who was running the bloodreavers. He came, up from secret passages beneath the toad statue, once Krand was bloodied in the Shrine. I had tonnes of Hobo Minions appear - and I used the Tougher Minion rules from the house rules forum, they worked really really well. Oh I converted some fo the kitchen area into cells and had some of the slaves there and had an elderly goblin accountant point the PCs in the Duergar's direction.
My Paldemar has contacted the reavers, deurgar and gnolls and has nearly figured out how to control all the bronze warders. He has given Murklemore the contract for providing security for the Hall and Thunderspire itself and he, eventally, plans to disrupt - or at least put up a Toll - the Trade Road between Cormyr and the Dales. So he is planning on having to defend himself from the Purple Dragons.
Not sure why he wants the gnolls, yet. But he has asked the Duergar to send some of the slaves to them as a "gift" - they'll be planning to hunt, eat or slaughter them I think. The Deurgar are using the slaves to help run the forges for amour, weapons and ore processing from their mines. I give the PCs 50xp for each slave they recover - I worked out three levels of major quests and had 50 slaves, err I think.
Anyway I plan on having Plademar pretty pissed that the bloodreavers have been wiped out - he wont know for a few days. As they were handy to have as slavers and agents outside of Thunderspire. I might have some rememnats of the Bloodreavers ambush the PCs in the Hall to rtry and get revenge. Oh and that Boar in with the gnolls I plan on giving to the PCs as a companion. I fugure the dwarf might want to ride that into battle.
Sorry for the brain dump - hope it provides you with some ideas you can use. I think Thunderspire is the best of the H adventures, although I haven't read them all, I really like the setting. But it feels half finished - lots of potential wasted, on the plus side it gives you a change to flex your creative muscle.