do a search for ranger pulled bedsides on google and some of the ranger forums, pulling the BII bed sides will be real similar
The hose you have now for your snorkel may be sufficient, I would test it out and see, the 2.9L doesnt suck that much air, but the longer the hose the more diameter is needed to move more air.
Get familiar with fiberglass, sheet metal and bondo if you want to really finish up your chop.
I think the plan for my BII is to keep the top, but have soft windows and a custom two piece tailgate, where the upper portion comes off.....but we'll see what I decide when it comes time to build my cage