A but more work required on the new cover to get the surface flat - I use a glass cutting board that is made of some hard to break glass and some oil on it to hold the "wet-n-dry' sand paper. I would finish with an oilstone, I have one large enough, you may not - in which case I'd get the cover flat with say 360grit and finish/polish with 800 (or even 1200 if I was not feeling too lazy).
It would seem I was correct in my suspicion of the grooves in the old cover - by the time you get those out there will be insufficient O-ring groove left.
To turn to your rods, are you trying to simply make them overall the same weight or are you trying to balance them "end for end".
If the latter - forget it, just balance for over all weight - I use a piece of bar with two holes drilled in the ends, I then make two wire hooks on which to hang the rods. Next I set the balance of the bar, with the hooks already fitted by simply moving the point where a third wire holds the bar.
Next I use my kitchen scales that are accurate to about .5g to get the rods close before hanging them on the hooks and removing metal from the heaviest until they balance.
if you are interested balancing "end-for-end" can be accomplished using the same basic setup but simply bending up a wire support to hold up the end of the rod you are not balancing.
It is a slow process and when you think you have the end-for-end correct, you need to re-check the overall balance.
BUT, whilst balancing the rods and pistons to the same weight will yield noticeable improvements in engine "smoothness' (lack of vibration), in the rev range that our bikes operate, end-for-end, not so much.
The last rods I balanced end-for-end were the ones in the KLE and then only because the overall weights were near identical and seeing as I had gone to all the trouble to make a balancing jig I wanted to use it. The end-for end was also very close, I initially made one pass with the angle grinder and made things worse, so most of the next 45 minutes was spent getting them back to being as good as they were before I messed with them.
Can't say I actually achieved anything as the KLE is a vertical parallel twin and would vibrate like 40 bastards except for the balancing shaft and I have neither time or equipment to start messing with that.
Sorry, forgot to say that up to the 11,500rpm redline it is very smooth, thinks almost entirely I suspect to the balance shaft.