Improving on a store bought kit

first time poster here, am i ever excited to find a great place to learn aobut the craft of brewing beer.

I have made one batch of beer with a Barons brew kit (mexican beer) and now am making my second batch (Dutch Lager). The first batch I made was not great after two weeks in the bottle but seemed good to me after four weeks. I have found now in this second go round that when moving the brew into the glass carboy that some of the grey muck that I put in at starting of the kit has transfered over. I will again try to make sure that I do not extract that to the bottles but as I move again into the primary fermenter I am sure that I can leave this behind this time as well.

I have a couple of questions, first with this second brewing I have had to add hops and they kind of were floating around when I transfered to the glass carboy. Is this normal? Also I was wondering if anyone has any tips to get the most out of these beer kits?

If I decide to try this process from scratch soon I was wondering if it is very hard to create a brew from scratch with my own ingredients?

I started out by doing extract recipes, which I would think is the next step up from the "all in One" kit. I was able to find all the ingredients at my Local Home Brew Store and, following the teachings of John Palmer's How to Brew, I was (and am) able to make a decent brew. I did not think that this process was hard at all. If you can keep things clean and neat, you can tell time, and you can boil water, you should be all set I am now doing extract w/steeping grains, and doing my first partial mash next time I brew, in advance of going All Grain.

As for the hops question, there are some who filter them out after the boil, some who leave them in. Were these the hops from the boil, or were you adding more? In either case, I don't think that it is a problem. I have added hops to my secondary and it worked out fine. I just made sure to bring as little of them as possible when I transferred to the bottling bucket. Next time, I think I might transfer them to another carboy a day or two in advance, to help get more out.

The biggest problem I have with many of the kits (but not all) is that they suggest adding some measure of sugar to the boil in order to up the abv (they get away with including less malt extract in the kit). If your kit suggests adding sugar to the boil I would instead add a measure of extract (liquid or dry) which will result in better flavor and more body.

As far as your own recipes it's not hard. Are you buying at a LHBS? If so, and the employees are worth their salt, they should be able to help you 'a la carte' a recipe or two from their inventory of malt, hops, and yeast.