I'm thinking I just need to wheel easier trails for a while until my skill develops.
I'm no expert (and who is really?), but after following your posts for some time, I think the comment above is the best solution and attitude to have.
Some of us were lucky enough to grow up on bikes from an early age. As a kid, I was too small for my first couple bikes and crashed plenty, simply for that reason. I didn't have the option to get a different bike or change much, so I just kept riding, had fun, and didn't over-think things.
OK, so you'd feel more comfortable if the bike was lower, I get that. My recommendation is this: Forget about physics and geometry and atleast re-consider a lowering-link. At this point in time, is a lowering-link really going to make a negative impact on your riding abilities? I know its not the "correct" thing to do (and I don't fault people for people telling you not to), but lets put this in perspective... you're a recreational trail rider and this is your first season riding. Not to mention that most people don't start out riding technical single track trails. A lowering link will have little or no bearing on your development at this point (or possibly ever).
I'm not against mods to personalize or dial-in a bike (as my bike is definitely not stock), but I'm just not seeing anything really wrong with the bike you've built, other than it may be a little tall for you.
If you added a lowering link (and adjusted the related fork height of course), you'd obviously notice the difference in height, but I believe anything beyond that would mostly be in your head. If you CAN tell a difference in handling, you'll adapt.
Going a bit further on the link topic... what specifically do you like about your OEM-height suspension now? What do you have to compare it to? How do you know it is setup properly as-is? The topic of suspension is a can of worms and is to some degree irrelevant when the common denominator in your struggles is you, not this bike.
I hope you don't think I'm picking on you, because thats really not my intent. Youre enthusiasm towards learning to ride and building a hybrid bike is really cool. I read your posts on RME and Motoutah and see how much fun you're having with this new hobby. However, I'd hate to see you get bogged down or overwhelmed with too much input and information, taking the fun out of it. Sure, there are setup changes and parts that will help you handle the bike better and boost your confidence, but there is no getting around paying your dues with crashes, and alot of them.
Speaking of crashes, I ride with some people that rarely ever crash (or don't at all anymore). Yeah, they're good riders, but they've also decided not to push themselves anymore and want to stay in their comfort zone or only stick to the trails they know. No matter what your skill level, if you don't crash (or have some close calls) from time to time, you're not riding hard enough to progress. Actually, I went riding this last weekend and put my bike down a couple times. They were preventable and I could have chosen easier routes, but I learned things that I wouldn't have if taking it easy.
Don't worry about any sort of "ideal" setup for now (if there is such a thing), as there will always be time later for that. Regardless of lowering links, auto-clutches, or anything else, focus most on getting out riding and gaining more experience.
Anyway, thats my .02.
