you definately need to replace the orifice tube when doing this changeover. It's in the line between the high and low side fittings where there is a nut to disconnect the lines. Write down which way the part comes out so you get the new one in the right way. The part is cheap, less than $10. It's the thing and filters the crud out of the system. Also, this part is why/how the high and low sides are on the same line. It acts as a throttling valve to cause a pressure change in the system. The "other" pressure change in the system in the compressor itself.
Also, once you get the system all together, do not open it back up. The accumulator is a desicant system that basically sucks the moisture out of the closed system. If you allow moisture in it, you basically should get a new accumulator.
Wherever you go to refill/recharge the system should apply vacuum to the line. This is how the system is tested for leaks as well as remove any moisture in the system. They will put it under vacuum for a while(should be at least a half hour) to get out any moisture then close the valve to the vacuum pump and leave the negative pressure in the lines and make sure the pressure doesn't change after 15 mins or so. This will verify no leaks in the system. Adding a small amount of freon doesn't really do anything to test for leaks unless you have some sort of leak detection system like a sniffer or dye test kit. Not to mention, the system really won't work without proper amount of 134a. Those do it yourself low-pressure guage kits are ok to just top things off(in my opinion) but a high and low pressure manifold guage is much better to add refrigerant and see how the system is taking it on the high and low side. (well...it takes it on the low side and will react on the high side...never try to put refrigerant in on high side b/c it'll try to pressuring the can more and can be dangerous)
best of luck to you....also, cleaning out the lines isn't "necessary" but it would sure stink to install a compressor yourself with no warranty and ruin it quickly because the system is full of crud. Don't even ask me why I'm giving this warning!!! I've done a number of AC jobs on my own and a few of my friends cars. Luckily I learned the hard way on my own car!! I guess it's possible the compressor I bought was bad(that's what I told to store to get another one) but thoroughly flushing the system did the trick for me.