I don't think I've ever done this, and If I have, I was probably a big nubcake. So here's how I'll do it: I will type a little thing up on the different parts, and then put my choice(s) at the end in parenthesis.
A bolt is a very important upgrade, there are a lot of them. the stock bolt is very heavy, causing massive kick... and not to mention is inefficient. Different bolts are good for different things though. The L6 is the most efficent, because of two tail O-rings. The DW hollowpoint, and the new V2 L7 bolt are the same weight now so are pretty much in a dead tie for cycle rate and recoil. Any of those three are my choices. (L6, L7, hollowpoint)
A board, In my opinion, is not a really needed upgrade. If you play in a league that requires a ramping setting then fine, but otherwise it's just flashy lights and modes you won't use. Despite this, my favorite board would have to be the APE Rampage board. It's back up to 130 now, but that's with good reason. The solenoid and hoses were just redesigned for higher pressures, and I believe the keypad was improved too. This board has infinite options, and the keypad is great. (APE Rampage)
Triggers are 100% preference. You need to try them out for yourself and decide.
The stock ion regulator (on most guns) is good. It is pretty consistent, and you won't get drop off with it if you keep it nice and lubed up. Some people end up with a **** one though, so in that case get a Dye Hyper 2. The price is really low now, and this this is +/= 1 or 2 at the chrono. (Dye Hyper II)
All feednecks work the same, just stay away from the twist locks and the Powerlyte. This should be your first upgrade.
There are a million of these. Get something with Purge, and an on/off. There are lots of different dropforwards and rail, try a bunch out to see what you like.
7. Barrel: http://www.pbnation.com/showthread.php?t=2218018
8. Air Source (tank):
Any tank will work with the Ion, Low Pressure or high. The problem with low pressure is that you can get major drop off if it doesn't have a really good regulator on it. I recommend sticking to high pressure, and getting a Carbon Fiber tank for the weight. CO2: You really should not use this unless you live in Nowheres ville, and absolutely can not get an air tank filled. You must either use Anti-Siphon on your regular co2 tank (your proshop can install it for you, very cheap) or use a remot line. DO NOT use both.
The Luck Stage 5, Stage 5.1, Trinity 08, and TechT Sleeper bodies are the true BOB ones. I recommend those.
Kila Magnetic Detents. No contest. Stay away from springs.
11. Trigger Frame:
There are a bunch, and they all function the same (basically...) Pick which you like the looks of best.
Clippard style for efficiency and SP 360 for ease. They both work great, you probably won't notice much of a performance difference between the two.
14. Gun Lubricant:
Anything dow 33. NO OIL... EVER. NO DOW 55... EVER.