The best way I've found for this G5, and in rebuilding mine I've taken off the processors a good 10 times... Put a small rice grain sized amount in the middle and either use a rubber glove or stretch plastic wrap over the tip of your finger and spread it around evenly. This prevents it from gooshing over the sides but still gets great contact. It'll still have some thickness and spread out nicely. Any other way you're guessing how much will cover the whole die. From the photo you have. doing it that way would get quite a bit on. A lot just acts as an insulator.
There are only 8 (if i remember right) capacitors on 2 sides (4 on either side of the die). Nothing too complex under that plastic shield and it's a fine distance away. Get some non-conductive paste (I use MX-4) and apply that and my vote is to still ditch the shield. Or, at least remove it and clean around the die really well and replace it.
I hope your rebuild goes better than my Dual pump attempt. Do post pics. The tubing runs are so short it's hard to get any extra tubing or splitters in there for any sort of fillport/t-line reservoir to bleed it.
This is a superior design, one pump for each processor and with separate chambers will get you better temps.
One method you can try if all else fails, get rid of those 'nubs' you were talking about and tap the hole with a G1/4 or M20 thread (common PC cooling threads) and buy a cheap threaded stop. This will allow you to fill it and bleed air for each chamber. Pretty much just like a PC reservoir where you'd attach threaded fittings
Best of luck.
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