Pod filters on 82 GPZ550, a number of questions.

If you are familiar with the OEM airbox, you likely like me think it is a pain to service carb removal and installation.
I managed to find a clean set of carbs at a low price, which I bought despite the fact I have the originals (with stiff diaphrams, was going to get new ones) and found another set at a reasonable price from a used part dealer which appeared to be in good shape but need a cleaning.
This latest set came with individual pod filters, since the carbs were so clean I decided to mount them and see if my bike would start up, it hadn't been run in 30+ years. Over the years I would drop a little oil in the cylinders and crank it over, otherwise never started. The bike fired up and ran rough, no surprise, that's how it always did, and after warming up purred like a kitten.
I checked all the jets, they are stock, although I can't say they weren't drilled out. It idles and giving it some gas appears to run right, but the bike is not yet road worthy so didn't hit the streets.
Questions:
1) If I run it like this, what should I do with the EGR tube, it pulls air from airbox and mixes it with exhaust gas I believe?
2) What about the crank case vent which would normally vent to the air box and get sucked by the carbs?
3) Manual says to turn the air screw out how many turns you screwed in, obviously I don't know what the carbs originally were, but my 30+ year memory is 1 1/2 turns, which is what these were. Bike does idle smoother as i turn them out, 1 1/2 seems about right.
4) I have always heard that bike will not run with pod filters, too lean, but at least at idle and giving it gas from idle appears to run smooth, if it does run too lean at spped, where should I start.

I can always take the pods off and reinstall the OEM airbox, even though I'll cuss like a sailer doing it.
 

Your bike has air injection, not EGR.  To remove, use a hose and connect the two ports on the valve cover, and plug any vacuum lines.  

Running your bike with stock jetting and pods will result in a lean mixture.  If the bike runs in this configuration, it will run hot, so don't do it.