Hi Rocklander,
First I must commend you on getting it all in the box
Re the output level issue;
Any time you have an Inverting last stage there is always the potential for transfer loss as you are then depending on the next stage Z to be high for max transfer. (not a comforting thought)
Please don't ask me to explain the in depth details as I'm not that clever at the deeper hidden meanings of electronics

But I've worn out 3 tu 4 breadboards in 30 odd years of messing with circuits and you get know what circuit ideas are full of holes.
Notice how Member *Mictester* is always banging the door down about *Buffer stages* ?? Well now you know Why. Winky.
If you want trouble free pedals it becomes obvious (even without a full understanding) that one needs to use buffers.
IME, use a non inverting stage as output will help but even then I've noticed there can still some transfer loss.
Even by adding a simple BJT follower would likely improve the situation.
Where you have Inter-stage coupling *inside a circuit* the issue would never arise as any loss is never going to be noticed BUT with pedals the In/Out/bypass difference can become problematic.
It may work on your setup but the moment you change the setup things can go belly up real quick.
As a working muso this is something you hardly need to have happen on stage.
The amount of dirt box schematics that hang a tone stage off the end with no buffer stage is just asking for signal loss issues to arise somewhere.
Sure they work but such ideas can be greatly improved.
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I've been messing with a trem/vibe circuit myself and with luck it should end up on this site one day but I'd like to worm out the bugs. My view is if you want it to work you have to spend a lot of time finding all the bugs.
I did have a listen to your sound clip and it certainly has the makings of something good though the tremolo was still very freq modulated. It seemed to have trouble getting that real volume up/down happening,, but hey still a useable effect.
I have no doubt that better qualified folk may well be able to give you a more definitive answer about the loss.
Phil.