I can't help you with the stock manifold removal (many others can though), as I've had tubular headers of one type or another on mine for about 9 years now. I can, however, suggest something you may want to consider though.....if you decide to pull the heads. I don't know if you are aware of the "dropped valve seat" issue on the early (05-06 and a few 07's) 5.7 Hemi's. If you're inclined and have the time/$$$, you may want to consider removing the heads and have new valve seats installed. IMO, it' fairly cheap insurance compared to the price of possibly a new engine if you do drop one. Plus, you can do it on your time schedule. You may want to do a search on this forum (and the internet) on "early Hemi dropped valve seats" if you're not familiar with this issue. Some forum members here have experienced this and hopefully will chime in with their experiences. Some weren't too bad and others...real bad.
I became real paranoid and anal about this with both my early 5.7 Hemi's, mostly because we travel quite a bit and didn't want to risk being stuck somewhere and end up at the mercy of a shop I knew nothing about. Hence, I pulled both of mine apart and had all the seats (and a bunch of other stuff) replaced. The set of heads on my lowest mileage Hemi (about 83K when torn down) was, according to the head repair shop, a definite candidate based on 2 of the intake seats started spinning in their pockets when he had them only about half way cut out.....too loose a fit in the head. Now, I feel about 99% sure I won't have to worry about this issue, plus I picked up a little more power. If you do this and keep the heads stock (I didn't since they were already off), the cost should only run about $900-1400 (I paid about $1800 per vehicle with all the mods.), depending on the market you're in.. A top end gasket kit costs about $200 from RockAuto.com.
In any case, if you don't pull it down, I would highly recommend you install a cooler thermostat and lower the cooling fan start temperatures to keep the engine from getting too hot......widely thought to be the primary cause of the dropped seats. The stock thermostat is 203* and the fans don't start coming on until about 225-230 degrees. Mine now never gets hotter than about 215*, even in our hottest weather 100-106*F) with the A/C on.
Good luck on whatever you do and let us know how it goes.