Germany will need to help Russia if they want resources. I assume that Russia and Germany become allies in the 1880s in this TL. At that time Russia barely had any industry and mines. Russia was a very backward country. Not very many railroads, very little industry, very little solid roads and armed forces that lagged years behind on those of western Europe. Germany will probably try to stimulate German companies and entrepreneurs to invest in Russia and they could try to make Nicholas II understand that modernisation is necessary. Wilhelm II of Germany was a very stubborn man. He might be able to do it. They could also train the Russian army and sell them modern equipment which they can copy and improve on. The Russian Empire had many resources and a huge population. Russia could have become a superpower if only the Russian rulers hadn't been so reactionary. If I had been Czar instead of Nicholas II, Russia would have beaten the crap out of tiny upstart Japan and Korea would have become a Russian province instead of a Japanese one.
Oh, those stereotypes!
Let's see it point by point.
1. Army: you see, Crimean war was had a great impact on the whole Russian society, and Russia had learned its lesson. In 1860-1870 there was a great reform in Army under war minister Milutin. From then on Russian Army became a conscript army instead of recruit army, and it was also rearmed with up-to-date weapons.
2. Industry: by 1890 the workers and proletarians occupied the main part of total Russian population - 51%. But, yes, over half of industry was light industry - esp. textile industry. But there were heavy industrial regions in Ural (Yekaterinburg, Chelyabinsk, Zlatoust), Poland, St. Petersburg, Nizhny Novgorod; major mining regions (East Ukraine, Ural etc). Totally, heavy industry was several times as less developed as in Germany but it developed rapidly due to home and foreign investment. Further German investments would help greatly but in OTL they diminished greatly after 1890. Yes, Russia was behind great European powers, in some spheres - far behind but I cannot say She was that backwards. Everything is recognised in comparison.
3. Roads. You see, in that time the USA, for example, didn't have much in a way of solid (cobbled or even asphalted) roads either (we don't speak of railroads here), but we cannot say they were backwards, it was just a specifics and geography. Russia in mid 90s had over 54 000 km of railroads, in 1991 it started Transsiberian railroad. So, by mid 90s Russia had built totally more railroads than Germany (compare with 1870 when Germany had total railroad length much more than Russia) and it built more occupying the 2nd place by the rates of railroad building after the USA. You'd say: of course, Germany is much smaller. Yes, Russia simply had to build more because she needed to cover its vast lands but there always were limits in money and people.
4. I would not call Russian Czars reactionary (In the day of his assasination, Alexander II was going to sign a Constitutional act limiting his powers as the absolute monarch - is it reactionary?
Well, you are welcome to explain what do you mean by that... IMHO, they may be called conservative.
If you were in Czar's boots, you'd had leaked the Japs you say? Well, how? You've got little populated areas in Far East, little industrial facilities, Transsib is one-way road interrupted at Baikal where you'll have to ship your troops by other means till they will be able to continue on rails to Vladivostok. You have no big naval power in the theatre at the start and you have the whole Japan near with quite short communications, able to react rapidly. You've got as the opponent on the sea one of the best and fortunate admirals of that time, Togo and don't have brainy admirals of your own on your side except Makarov but he's going to be killed in unfortunate accident in early war...
But I'm sure that some-one will say that Italy is the soft underbelly of the Central Powers
Someone named Winston Churchill told that about Balkans...