You can just finish the wood with a waterborne polyurethane over a sealer or natural stain...and the floor will be lighter than your golden oak cabinets. Or...color the wood and then finish with a waterborne polyurethane.

Without pictures it will be hard for us to visualize what just happened. At this point, you are not ready to throw down a finish (or a sealant). It sounds like you have not picked a finish (as in have not investigated it let alone purchased it). Without the finish, you are "sealing blind". First things first: Rule #1: Never (ever) mix brands/materials when working with finishes/stains/sealants. Stick with ONE LINE of product (ie. Bona or Loba, or Glitza, etc). Rule #2: Pick your finish FIRST and then figure out if the FINISH requires a sealant. Purchase ONLY the materials LISTED by the manufacturer of the FINISH. If it REQUIRES IT then you MUST use it. If it is not required but it doesn't do any harm, then you can skip it. Rule #3: Know all of this before sanding. The finish/sealant will have sanding REQUIREMENTS that the manufacturer states right on the can/website. Rule #4: Always follow the instructions for "open time", flash time, dry time and cure time listed. Rule #5: Know the manufacturer's requirements for the species of wood you are refinishing (eg. white oak needs a sealant when working with water based polyurethane whereas red oak does not...not normally anyway). Rule #6: Always follow the manufacturer's (of the finish) advice on how to go about applying the finish (this includes applicator and sanding requirements). As you can see, the "requirements" will depend on the FINISH you choose. If you have not chosen a finish, then you won't be able to do any of the above (that includes sanding). I know for a fact that Bona, Loba and Rubio Monocoat all have sanding requirements. And each one is different. The 'basics' are the same (three grit levels are required = at least 3 passess of the sanding machine/edge sander) but the specifics are very different (which level to START WITH and which one to END WITH). For finishes, I prefer the HIGH END European polyurethane like Loba 2K Supra AT (ceramic infused polyurethane) because of its high scratch resistance. The down side is the price ($170/gallon). The Bona line has some awesome products at a slightly cheaper rate, but the down side is the BIG problems with the short working time (2 minute wet edge = professional level experience + T-bar applicator knowledge). Please stay away from Minwax. Varathane is only one step up. DuraSeal is a DIY friendly finish with a decent price tag and easy working times (10 minute wet edge). Good luck. Please stop sanding/sealing until you have purchased your finish. You can start everything once you've had a chance to read the instructions on the can. Be prepared to have to do another "finishing pass" with the sanding machine. This is quite common if you didn't have the finish purchased before you started.

I paid to have an independent, certified flooring inspector come in to evaluate my floors. His final report noted that the pinholes were caused by an improper finish. The flooring contractor applied 2 coats of polyurethane on the same day and did not allow sufficient time for the first coat to fully dry before they applied the second coat. The inspector noted a hazed appearance in numerous areas that were indicative of the previous coat not being fully dry before the second coat was applied. The wood was not a number 2 grade selection and the inspector contacted a technical adviser from the National Wood Flooring Associate and he said that there was nothing inherent to the red oak that would have caused the extensive pinholing in the finish that was observed and that this was due to either incompatible finish products being used or improper application procedures. I had a second company come in and redo the entire refinish - sanding down to bare wood and reapplying stain and 3 coats of poly and there are no pinhole visible on any floors in the house. The fact that the issue could be corrected by completing redoing the work lends credence to the original job having been poorly done. The original company tried applying a 4th coat of polyurethane but this did nothing to fix the pinholes. If you look at page 59 of this PDF, pinholes can appear in the finish of a floor if the previous coat was not fully dry (http://www.crescenthardwood.com/nwfa/ProblemsCauses.pdf). The bottom line was that I was out a lot of money from the first contractor, which was a large reputable company in my area, because they refused to fix the issue or even test to see if their finish job was the issue and had to go through the aggravation of having the entire job redone. The second company came out and sanded the floor of a closet and reapplied stain and 3 coats of poly to ensure that it was the previous finish and not inherent to the wood. The test area showed that when done correctly no pinholes in the finish formed.

classychic563 I realize this is an old thread but I was out of town and just checking old posts now. I saw that you're thinking of getting stain pens? as in those felt tip markers? I hope you didn't. they won't penetrate the top coat, the area is too large and besides, those pens are total crap. I can never get them to match, even for tiny scratches. don't think about topping it with gel stain either. it will never look right. I am a somewhat experimental DIYer willing to take some risks, and even I would not attempt to tackle this project myself, not on fresh new floors. you had a question on where to find such good, artistic woodworkers -- I don't know. here's where I would try: google "wood restoration" in your area and ask them if they do floors and if they don't, ask them for referrals. vet them carefully. ask to see before and after pics of their work (specifically, pics of spot repair where they did not redo the entire area). ask friends and neighbors for personal recommendations too.