Welcome to FT, you're going to learn a lot. My answers are in bold

1. Seems like the Chase Freedom card would be a good option to build extra points with their categories. Is there any downside to applying for one so soon after applying and receiving the Sapphire Reserve I got??
Chase has a 5 applications in 24 months rule so that could be an issue or not for you. It'll also be another hardpull on your credit which is something you'll have to consider.

2. I would like to go to Europe after the summer this year, probably starting in Rome, I am in Houston. Im sure there’s a number of airlines that go there, but how can I fully explore all my options that I can use my UR points for? For example, looking at United’s website they also have flights from Lufthansa while Lufthansa isn’t listed as one of the 11 UR transfer partners. I think I read somewhere also that British Airways was used to book on some airlines as well with Avios or UR points transferred into Avios. How can I work out these details?
Each airline program has its own list of redemption partners and rates. If you were to transfer Chase UR points to UA's MileagePlus program you can then use those miles to redeem on UA and/or it's partners. You're a bit late to the game already for summer travel but it's still possible to do. Award travel opens about ~330 days before you wish to travel so people have a several month jump on you. You'll have to earn the points, find the availability and book what is available.

3. Do the transfer partners let you pay part points and part credit card for example? i.e. if a fare is cheap in either points or $$, is it reflected in the other?
Each airline & program has it's own rules on this. In many programs the redemption rate is based on a chart based on departure & destination not distance or dollars but some do offer a cash+points payment option

4. For the many specials I see with cheap economy fares on sites like The Points Guy, does this mean that typically the business or first class options are normal price, or can one make an assumption that there are deals to be had for business / first on these flights as well?
You can never assume either way. You just have to check. Here on FT and some other sites they do have a Premium fare special section.

5. I own a small business and I would love a card with bonus points for things like mechanics, maintenance etc since it’s transportation related. I haven’t seen any of these but there seems to be some options for gas bonuses. Obviously there’s the Ink business cards and then there is the AMEX simply cash card which would give 3X on fuel, there’s also the Gold Amex for 3x on fuel. However, I am leaning away from getting another premium card with a high yearly fee since I just got one. What suggestions do people have? I would be looking for something that gives Membership Rewards Points
Can't help you there. You want MR but don't want a "high fee" card. You either have to pay or settle for the lower earnings. Right now I'd say stay with a Chase UR centric earning as you're very new to this. Once you've learned to crawl you can walk around.

6. I hear good things about the SPG starwood points, however the card seems to only give bonuses on hotel stays which I don’t think I would spend a lot on in a year. Am I missing something is the fact that that even at 1X they are still valuable and I should try and earn them?
The SPG card and it's soon to be related Marriott & Ritz Carlton cards are great for their transfer flexibility to airline programs & SPG redemptions but the earning rate as you said isn't great in general. It's great for those that stay at SPG properties. Getting an SPG card & a Marriott card (A chase card so watch that 5 in 24 rule) you can get a lot of points via the signup bonuses but it'll be kind of a loss in the end if you don't use the card or don't stay at those properties.

7. MY goal with diversifying my points is so I have different options for airlines to transfer them to and to make sure I am getting the most benefit for my current spending habits. After UR what point currency would be a good option for me to concentrate on?
I recomment to start off small and learn to maximize one program before you spread it around. You don't want to end up with 4 ponds of points that can't get you where you want instead of 1 or 2 big lakes worth.

8. Next year in 2018 I would like to goto New Zealand & Australia. Since this is obviously a long flight, I would like to have a game plan formulated for flying at a minimum business but preferably first class. I am open to dates, so Im not limited by going at a certain time of year. While there are some options via UR points Im curious if anyone has suggestions of other point programs and airlines.
This is where the two pools of points will probably come in handy. Using something like AA & UA points which each allow for 1 way awards. This gives you flexibility on getting to and from where you want to go with less constriction to availability as you have more redemption offers. Start planning as soon as availability opens.

9. I have some property taxes due this month, to pay with a credit card will cost me an additional 2.15%. However, I know in some instances points can be worth more than that when redeeming. What’s everyone’s thoughts on doing this?
This is dependent upon your view of value, need for points & how much you could earn. Some people use some services to pay all bills that charge fees but gain large amounts of points which they use for premium redemptions

10. How can I go about beginning to look for dates and “good deals” for redemption for business or first class flights?
Reading the stickies on the airline programs and airlines you wish to fly.

11. I have heard of excursions, basically extended layovers where you can stay in a location for a certain time and then continue on to another destination without extra cost. Can someone explain how this works and what it’s limitations are?
There are layovers, stopovers & open jaw options. A layover is generally less than 24 hours in an area and some programs/airlines allow for anywhere from none to several during a trip. A stopover is usually a few days in one area before continuing on your path to your destination. Some programs allow these and others charge fees and some do not allow for these. An open jaw ticket is when you fly for example JFK-LHR and then BCN-JFK and you arrange travel between the two cities on your own.

12. Should I go ahead and create frequent flyer accounts for the transfer partners that UR uses now so I don’t have to worry about it later?
You can/should make accounts with the program you determine to help you best redeem and also those that are good for searching. For Star Alliance airlines people often use UA & AC's programs to search for award availability. I like UA & NH myself. For OneWorld the search limitations go further. AA is good for some, BA is good for others. Latam availability can be difficult to find so getting an account with them can help if you're going to South American just for searching. For Skyteam I use AF & DL for searching.

Sorry for this lengthy post. I am new to this and so I naturally have a lot of questions and I would appreciate peoples’ input on these questions.


Thanks![/QUOTE]

There is a glossary under the "help" section of FT that can help you with learning the jargon used here and in air travel.